Methods for the treatment of infections and tumors

ABSTRACT

PD-1 antagonists are disclosed that can be used to reduce the expression or activity of PD-1 in a subject. An immune response specific to an infectious agent or to tumor cells can be enhanced using these PD-1 antagonists in conjunction with an antigen from the infectious agent or tumor. Thus, subjects with infections, such as persistent infections can be treated using PD-1 antagonists. In addition, subjects with tumors can be treated using the PD-1 antagonists. In several examples, subjects can be treated by transplanting a therapeutically effective amount of activated T cells that recognize an antigen of interest and by administering a therapeutically effective amount of a PD-1 antagonist. Methods are also disclosed for determining the efficacy of a PD-1 antagonist in a subject administered the PD-1 antagonist. In some embodiments, these methods include measuring proliferation of memory B cells in a sample from a subject administered the PD-1 antagonist.

PRIORITY CLAIM

This application is a continuation of U.S. patent application Ser. No.12/626,848, filed Nov. 27, 2009, which claims the benefit of U.S.Provisional Patent Application No. 61/118,570 filed Nov. 28, 2008, bothof which are incorporated by reference herein in their entirety.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under grant numbers RO1AI057029, RO1 AI071852 and RO1 AI074417 awarded by the NationalInstitutes of Health. The government has certain rights in theinvention.

FIELD

This application relates to the use of antagonists, specifically to theuse of PD-1 antagonists for the treatment of persistent infections andtumors, and to methods for determining an effective dose of a PD-1antagonist.

BACKGROUND

Immunosuppression of a host immune response plays a role in persistentinfection and tumor immunosuppression. Persistent infections areinfections in which the virus is not cleared but remains in specificcells of infected individuals. Persistent infections often involvestages of both silent and productive infection without rapidly killingor even producing excessive damage of the host cells. There are threetypes of persistent virus-host interaction: latent, chronic and slowinfection. Latent infection is characterized by the lack of demonstrableinfectious virus between episodes of recurrent disease. Chronicinfection is characterized by the continued presence of infectious virusfollowing the primary infection and can include chronic or recurrentdisease. Slow infection is characterized by a prolonged incubationperiod followed by progressive disease. Unlike latent and chronicinfections, slow infection may not begin with an acute period of viralmultiplication. During persistent infections, the viral genome can beeither stably integrated into the cellular DNA or maintained episomally.Persistent infection occurs with viruses such as human T-Cell leukemiaviruses, Epstein-Barr virus, cytomegalovirus, herpesviruses,varicella-zoster virus, measles, papovaviruses, xenotropic murineleukemia virus-related virus (XMRV), prions, hepatitis viruses,adenoviruses, parvoviruses and papillomaviruses.

The mechanisms by which persistent infections are maintained can involvemodulation of virus and cellular gene expression and modification of thehost immune response. Reactivation of a latent infection may betriggered by various stimuli, including changes in cell physiology,superinfection by another virus, and physical stress or trauma. Hostimmunosuppression is often associated with reactivation of a number ofpersistent virus infections.

Many studies show defective immune responses in patients diagnosed withcancer. A number of tumor antigens have been identified that areassociated with specific cancers. Many tumor antigens have been definedin terms of multiple solid tumors: MAGE 1, 2, & 3, defined by immunity;MART-1/Melan-A, gp100, carcinoembryonic antigen (CEA), HER-2, mucins(i.e., MUC-1), prostate-specific antigen (PSA), and prostatic acidphosphatase (PAP). In addition, viral proteins such as hepatitis B(HBV), Epstein-Barr (EBV), and human papilloma (HPV) have been shown tobe important in the development of hepatocellular carcinoma, lymphoma,and cervical cancer, respectively. However, due to the immunosuppressionof patients diagnosed with cancer, the innate immune system of thesepatients often fails to respond to the tumor antigens.

Both passive and active immunotherapy has been proposed to be of use inthe treatment of tumors. Passive immunity supplies a component of theimmune response, such as antibodies or cytotoxic T cells to the subjectof interest. Active immunotherapy utilizes a therapeutic agent, such asa cytokine, antibody or chemical compound to activate an endogenousimmune response, where the immune system is primed to recognize thetumor as foreign. The induction of both passive and active immunity havebeen successful in the treatment of specific types of cancer.

In general, a need exists to provide safe and effective therapeuticmethods and to establish safe dosing of agents to treat disease, forexample, autoimmune diseases, inflammatory disorders, allergies,transplant rejection, cancer, immune deficiency, viral infections andother immune system-related disorders. There also remains a need formethods for determining if a particular dose of a therapeutic agent,such as a PD-1 antagonist, is effectively treating a subject.

SUMMARY

PD-1 antagonists reduce the expression and/or activity of PD-1. Subjectswith infections, such as persistent infections can be treated using PD-1antagonists. Subject with tumors can also be treated using PD-1antagonists. Additionally, subjects can be treated by transplanting atherapeutically effective amount of activated T cells that recognize anantigen of interest in conjunction with a therapeutically effectiveamount of a PD-1 antagonist.

An immune response can be measured in the mammalian recipient. In someembodiments the method of treatment disclosed herein includes measuringB cells. In some embodiments, the methods include measuring theproliferation of memory B cells in a sample from the subject.

In some embodiments, methods are disclosed for determining the efficacyof a PD-1 antagonist in a subject administered the PD-1 antagonist.These methods include measuring proliferation of memory B cells in asample from a subject administered the PD-1 antagonist, wherein anincrease in proliferation of memory B cells from the sample as comparedto a control indicates that the PD-1 antagonist is efficacious fortreating the subject.

Methods for determining the dose of a PD-1 antagonist that is useful totreat a subject are also disclosed herein. These methods includeadministering to the subject a first dose of a PD-1 antagonist, anddetermining the proliferation of memory B cells in a first sample fromthe subject. An increase in the proliferation of memory B cells from thefirst sample as compared to a control indicates that the first dose ofthe PD-1 antagonist is of use treating the subject. An absence of asignificant alteration in the proliferation of memory B cells ascompared to the control indicates that the first dose of the PD-1antagonist is not sufficient to treat the subject.

The foregoing and other features and advantages will become moreapparent from the following detailed description of several embodiments,which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1C. FIG. 1A is a bar graph showing the levels of PD-1 mRNA inD^(b)GP33-41 and/or D^(b)GP276-286 specific T cells from naïvetransgenic mice, lymphocytic choriomeningitis virus (LCMV) Armstrongimmune (approximately 30 days post-infection) infected mice, orCD4-depleted LCMV-Cl-13 infected mice (approximately 30 dayspost-infection), as measured by gene array analysis. FIG. 1B is a seriesof images of a flow cytometry experiment showing PD-1 surface expressionon CD8+ tetramer+ T cells in LCMV Armstrong immune and CD4 depletedLCMV-Cl-13 infected mice approximately 60 days post-infection. AnergicCD8+ T cells express high levels of PD-1 polypeptide on the cell surfaceapproximately 60 days after chronic infection with LCMV-Cl-13 virus(labeled “chronic”), but virus-specific CD8+ T cells do not express PD-1polypeptide after clearance of an acute LCMV Armstrong infection(labeled “immune”). FIG. 1C is a series of images of a flow cytometryexperiment demonstrating the presence of PD-L1 on splenocytes fromchronically infected and uninfected mice. It demonstrates that PD-L1expression is the highest on the splenocytes that are infected by thevirus.

FIGS. 2A-2E. FIG. 2A is a series of scatter plots showing that whenCl-13 infected mice are treated from day 23 to 37 post-infection therewas approximately a 3 fold increase in the number of DbNP396-404specific and DbGP33-41 specific CD8+ T cells compared to the untreatedcontrols. In order to determine any changes in function IFN-γ and TNF-αproduction was measured in response to 8 different LCMV epitopes. FIG.2B is a scatter plot showing that when all the known CD8+ T cellspecificities are measured there is a 2.3 fold increase in total numberof LCMV specific CD8+ T cells. FIG. 2C is a series of flow cytometrygraphs showing IFN-γ and TNF-α production in response to eight differentLCMV epitopes. FIG. 2D is a scatter plot showing that more virusspecific CD8+ T cells in treated mice have the ability to produce TNF-α.FIG. 2E is a series of bar charts showing that PD-L1 blockade alsoresulted in increased viral control in the spleen liver lung and serum.

FIGS. 3A-3D. FIG. 3A is a graph demonstrating the increase in DbGP33-41and DbGP276-286 specific CD8+ T cells (labeled “GP33” and “GP276”) inCD4-depleted C1-13 infected mice treated with anti-PD-L1 (labeled“αPD-L1”) from day 46 to day 60 post-infection versus control (labeled“untx”), which demonstrates that mice treated with anti-PD-L1 containedapproximately 7 fold more DbGP276-286 specific splenic CD8+ T cells andapproximately 4 fold more DbGP33-41 specific splenic CD8+ T cells thanuntreated mice. FIG. 3B is a series of images of a flow cytometryexperiment demonstrating the increased frequency of DbGP33-41 andDbGP276-286 specific CD8+ T cells in the spleen of CD4-depleted C1-13infected mice treated with anti-PD-L1 (labeled “αPD-L1 Tx”) from day 46to day 60 post-infection versus control (labeled “untx”). FIG. 3C is aseries of images of a flow cytometry experiment demonstrating increasedproliferation of DbGP276-286 specific CD8+ T cells in anti-PD-L1-treatedmice, as measured by BrdU incorporation and Ki67 expression. FIG. 3D isa chart showing that mice having high levels of CD8+ T cell expansiondemonstrate an appreciable response in peripheral blood mononuclearcells (PBMC), as shown by comparing DbGP276-286 specific CD8+ T cells inthe PBMC as compared to DbGP276-286 specific CD8+ T cells in the spleen.

FIGS. 4A-4E. FIG. 4A is a series of charts demonstrating the increase inIFN-γ producing DbGP276-286 and DbGP33-41 specific CD8+ T cells inanti-PD-L1-treated mice, as compared to controls. Higher frequencies ofDbNP396-404, KbNP205-212, DbNP166-175, and DbGP92-101 specific CD8+ Tcells were also detected in anti-PD-L1-treated mice. FIG. 4B is a chartdemonstrating that in anti-PD-L1-treated mice, 50% of DbGP276-286specific CD8+ T cells produce IFN-7, as compared to 20% of DbGP276-286specific CD8+ T cells in control mice. FIG. 4C is a series of images ofa flow cytometry experiment demonstrating that anti-PD-L1-treatedchronically infected mice produce higher levels of TNF-α than untreatedchronically infected mice, but still produce lower levels of TNF-α thanimmune mice infected with LCMV Armstrong virus. FIG. 4D is a chartdemonstrating that treatment of LCMV-Cl-13 infected mice with anti-PD-L1renews ex vivo lytic activity of the virus-specific T cells, as comparedto untreated infected mice, measured using a ⁵¹Cr release assay. FIG. 4Eis a series of charts demonstrating the reduction of viral titers invarious organs following treatment of LCMV-Cl-13 infected mice withα-PD-L1. Viral titers decreased approximately 3 fold in the spleen, 4fold in the liver, 2 fold in the lung, and 2 fold in serum after 2 weeksof anti-PD-L1 treatment, as compared to untreated mice.

FIGS. 5A-5D. FIG. 5A is a series of images of a flow cytometryexperiment showing PD-1 surface expression using 10 HIV tetramersspecific for dominant epitopes targeted in chronic Glade C HIVinfection. The percentages indicate the percentage of tetramer⁺ cellsthat are PD-1⁺. FIG. 5B is a series of charts demonstrating that thepercentage and MFI of PD-1 is significantly upregulated on HIV-specificCD8+ T cells compared to the total CD8+ T cell population (p<0.0001) inantiretroviral therapy naïve individuals, and PD-1 is increased on thetotal CD8+ T cell population in HIV-infected versus HIV-seronegativecontrols (p=0.0033 and p<0.0001, respectively). 120 HIV tetramer stainsfrom 65 HIV-infected individuals and 11 HIV seronegative controls wereincluded in the analysis. FIG. 5C is a series of charts showing themedian percentage and MFI of PD-1 expression on tetramer⁺ cells byepitope specificity. FIG. 5D is a chart depicting the variation in thepercentage of PD-1⁺ cells on different epitope-specific populationswithin individuals with multiple detectable responses. Horizontal barsindicate the median percentage of PD-1⁺ HIV tetramer⁺ cells in eachindividual.

FIGS. 6A-6D. FIG. 6A is a series of charts demonstrating that there isno correlation between the number of HIV-specific CD8+ T cells, asmeasured by tetramer staining, and plasma viral load, whereas there is apositive correlation between both the percentage and MFI of PD-1 ontetramer⁺ cells and plasma viral load (p=0.0013 and p<0.0001,respectively). FIG. 6B is a series of charts showing that there is nocorrelation between the number of HIV tetramer⁺ cells and CD4 count,whereas there is an inverse correlation between the percentage and MFIof PD-1 on HIV tetramer⁺ cells and CD4 count (p=0.0046 and p=0.0150,respectively). FIG. 6C is a series of charts demonstrating that thepercentage and MFI of PD-1 on the total CD8+ T cell populationpositively correlate with plasma viral load (p=0.0021 and p<0.0001,respectively). FIG. 6D is a series of charts depicting the percentageand MFI of PD-1 expression on the total CD8+ T cell population isinversely correlated with CD4 count (p=0.0049 and p=0.0006,respectively).

FIGS. 7A-7B. FIG. 7A is a series of images of a flow cytometryexperiment showing representative phenotypic staining of B*4201TL9-specific CD8+ T cells from subject SK222 in whom 98% of B*4201TL9-specific CD8+ T cells are PD-1⁺. FIG. 7B is a chart illustrating asummary of phenotypic data from persons in whom >95% of HIV-specificCD8+ T cells are PD-1⁺. Seven to 19 samples were analyzed for each ofthe indicated phenotypic markers. The horizontal bar indicates medianpercentage of tetramer⁺ PD-1⁺ cells that were positive for the indicatedmarker.

FIGS. 8A-8C. FIG. 8A is a series of images of a flow cytometryexperiment showing the representative proliferation assay data from aB*4201 positive subject. After a 6-day stimulation with peptide, thepercentage of B*4201 TL9-specific CD8+ T cells increased from 5.7% to12.4% in the presence of anti-PD-L1 blocking antibody. FIG. 8B is a linegraph depicting the summary proliferation assay data indicating asignificant increase in proliferation of HIV-specific CD8+ T cells inthe presence of anti-PD-L1 blocking antibody (n=28, p=0.0006, pairedt-test). FIG. 8C is a bar graph showing the differential effects ofPD-1/PD-L1 blockade on proliferation of HIV-specific CD8+ T cells on anindividual patient basis. White bars indicate fold increase of tetramer⁺cells in the presence of peptide alone, black bars indicate the foldincrease of tetramer⁺ cells in the presence of peptide plus anti-PD-L1blocking antibody. Individuals in whom CFSE assays were performed formore than one epitope are indicated by asterisk, square, or trianglesymbols.

FIGS. 9A-9D are a diagram and a set of graphs showing the synergisticeffect of therapeutic vaccine combined with PD-L1 blockade onantigen-specific CD8-T cell frequency and viral titer in chronicallyinfected mice. FIG. 9A is a schematic diagram of an experimentalprotocol. LCMV clone-13 (CL-13)-infected mice were vaccinated withwild-type vaccinia virus (VV/WT) or LCMV GP33-41 epitope-expressingvaccinia virus (VV/GP33) at 4 (week) post-infection. At the same time,the mice were treated 5 times every three days with or withoutanti-PD-L1. FIG. 9B is a series of images of a flow cytometry experimentshowing the frequency of GP33- and GP276-specific CD8-T cells in PBMC at1-wk post-therapy. The number represents frequency of tetramer-positivecells per CD8-T cells. Data are representative of three experiments.FIGS. 9C-9D are graphs of the frequency of GP33- and GP276-specificCD8-T cells (FIG. 9C) and viral titers (FIG. 9D) in the bloodpost-therapy. Changes in the numbers of tetramer-positive CD8-T cellsand the viral titers were monitored in the blood by tetramer stainingand plaque assay, respectively, at the indicated time points. Thenumbers of tetramer-positive CD8-T cells and viral titers are shown forindividual (upper four panels) and multiple (lower panel) mice followinginfection with VV/WT or VV/GP33 (straight line) and treatment withanti-PD-L1 (shade region). Dashed lines represent virus detection limitResults are pooled from three experiments.

FIGS. 10A-10D are graphs and digital images showing increasedantigen-specific CD8-T cells and enhanced viral control in differenttissues of the mice given therapeutic vaccine combined with PD-L1blockade. FIG. 10A is a series of images of a flow cytometry experimentshowing the frequency of GP33-specific CD8-T cells in different tissuesat 4-wk post-therapy. The number represents frequency of GP33tetramer-positive cells per CD8-T cells. Data are representative of twoexperiments. FIG. 10B is a graph of GP33-specific CD8 T-cell numbers indifferent tissues at 4-wk post-therapy. FIG. 10C is a set of bar graphsshowing viral titers in the indicated tissues at 2 (filled)- and 4(blank)-wk post-therapy. Dashed lines represent virus detection limitn=6 mice per group. Results are pooled from two experiments. FIG. 10D isa digital image of immuno-staining of spleen with aLCMV antigens (red)at 2-wk post-therapy. Magnification, ×20.

FIGS. 11A-11D are plots and graphs showing enhanced restoration offunction in exhausted CD8-T cells by therapeutic vaccine combined withPD-L1 blockade. FIG. 11A is a series of images of a flow cytometryexperiment showing IFN-γ production and degranulation by splenocytes ofthe vaccinated mice at 4-wk post-therapy. Splenocytes were stimulatedwith the indicated peptides in the presence of αCD107a/b antibodies andthen co-stained for IFN-γ. The shown plots are gated on CD8-T cells andare the representative of two independent experiments. FIG. 11B is agraph showing the percentage of IFN-γ⁺CD107⁺ cells per CD8-T cellsspecific for each of LCMV peptides from FIG. 11A are summarized formultiple mice (n=6 for each response). Results are pooled from twoexperiments. FIG. 11C is a set of plots showing TNF-α production fromCD8-T cells capable of producing IFN-γ in the vaccinated mice. Afterstimulation of splenocytes with GP33-41 or GP276-286 peptide,IFN-γ-producing CD8-T cells were gated and then plotted by IFN-γ(x-axis) versus TNF-α (y-axis). The upper and lower numbers on plotsindicate frequency of TNF-α⁺ cells among IFN-γ⁺ cells and meanfluorescent intensity (MFI) of IFN-γ⁺ cells, respectively. The data arerepresentative of two independent experiments. FIG. 11D is a graphshowing the percentage of TNF-α⁺ cells per IFN-γ⁺ cells for GP33-41 orGP276-286 peptide from FIG. 11C are summarized for multiple mice (n=6for each response).

FIGS. 12A-12B are a set of plots showing the effect of a therapeuticvaccine combined with PD-L1 blockade changes phenotype ofantigen-specific CD8-T cells of chronically infected mice. FIG. 12A is aset of plots showing the phenotype of GP33 tetramer-specific CD8-T cellsin PBMC at the indicated times post-therapy. Histograms were gated onGP33⁺ CD8-T cells. Frequency of population expressing high-level of CD27or CD127 is indicated by percent on plots. The numbers on histograms ofGranzyme B represent MFI of expression. The data are representative ofthree independent experiments. FIG. 12B is a set of plots showingphenotypic changes of GP33 tetramer-specific CD8-T cells in differenttissues at 4-wk post-therapy. Histograms were gated on GP33⁺ CD8-Tcells. Frequency of population expressing high-level of CD127 or PD-1 isindicated by percent on plots. The numbers on histograms of Granzyme Band Bcl-2 represent MFI of expression. The data are representative oftwo independent experiments.

FIGS. 13A-13E are a schematic diagram, plots and graphs showing thesynergistic effect of therapeutic vaccine combined with PD-L1 blockadeon restoration of function in ‘helpless’ exhausted CD8 T cells. FIG. 13Ais a schematic diagram of the protocol. Mice were depleted of CD4 Tcells and then infected with LCMV clone-13. Some mice were vaccinatedwith wild-type vaccinia virus (VV/WT) or LCMV GP33-41 epitope-expressingvaccinia virus (VV/GP33) at 7-wk post-infection. At the same time, themice were treated 5 times every three days with αPD-L1 or its isotype.Two weeks after initial treatment of antibodies, mice were sacrificedfor analysis. FIG. 13B is a series of images of a flow cytometryexperiment and a bar graph showing the frequency of GP33-specific CD8-Tcells in the indicated tissues at 4-weeks post-therapy. The numberrepresents frequency of GP33 tetramer-positive cells per CD8-T cells.Frequency of GP33-specific cells per CD8 T-cells in different tissues at2-weeks post-therapy is also summarized. FIG. 13C is a series of imagesof a flow cytometry experiment showing the results from experimentswherein splenocytes stimulated with GP33 peptide in the presence ofαCD107a/b antibodies and then co-stained for IFN-7. The shown plots aregated on CD8-T cells. The percentage of IFN-γ⁺CD107⁺ cells per CD8-Tcells specific for GP33 peptide are summarized for multiple mice. FIG.13D is a bar graph of the percentage of IFN-γ⁺ cells after stimulationwith GP33 peptide per cells positive for Db-restricted GP33-41 tetramerare summarized for multiple mice. FIG. 13E is a bar graph of viraltiters in the indicated tissues at 2-wk post-therapy. All plots arerepresentative of two experiments and all summarized results are pooledfrom two experiments (n=6 mice per group).

FIGS. 14A-14B are a set of plots and graphs showing that blockade of thePD1/PD-L1 signaling pathway increases the total number ofantigen-specific T cells following adoptive transfer into congenitalcarrier mice. Whole splenocytes were adoptively transferred intocongenital carrier mice with or without therapy with anti-PD-L1. FIG.14A is a set of representative flow cytometry plots from specifictime-points gated on CD8+ T cells. FIG. 14B are graphs showing thekinetics of Db GP33-specific CD8 T cell expansion in peripheral bloodfrom two independent experiments (n=4 animals per group) FIGS. 15A-15Eare plots and graphs showing that blockade of the PD-1/PDL1 pathwayfollowing adoptive T cell immunotherapy enhances cytokine production inantigen specific CD8 T cells. Splenocytes were isolated at day 17post-transfer and analyzed for cytokine expression upon stimulation withantigenic peptide. FIG. 15A is a set of representative flow plots areshown for the expression of IFNγ assessed by intracellular cytokinestaining following 5 hours of stimulation with defined CD8 epitopes orno peptide controls. FIGS. 15B and 15D are representative plots areshown for the dual expression of TNFα or 107ab and IFNγ (quadrant statsare percentage of CD8 gate). FIGS. 15C and 15E are graphs of thepercentage of IFNγ producing cells also producing TNFα or 107ab (n=3animals per group)

FIGS. 16A-16B are a graph and plots showing increased levels of AntibodySecreting cells in LCMV Clone-13 infected mice. Total ASC levels weremeasured in chronic LCMV infected mice following αPD-L1 treatment byELISPOT and CD138 staining. FIG. 16A is a graph of total number ofsplenic ASC, summary of results from three independent experiments. FIG.16B is a set of plots showing an increase in antibody secreting cells(ASC) in the spleen can be measured by the marker CD138. Showing onerepresentative plot, ASC are CD138+ and B220 low/intermediate (gated onlymphocytes).

FIG. 17 is a graph showing treatment of chronic LCMV infected mice withanti-PD-L1 does not lead to elevated levels of bone marrow ASC. Totalnumbers of ASC were enumerated from the spleen and bone marrow ofchronic LCMV infected mice 14 days post anti (α)PD-L1 treatment byELISPOT. Line represents geometric mean within the group.

FIG. 18 is a graph showing that co-administration of αPD-L1 and αCTLA-4leads to synergistic increases in splenic ASC. Chronic LCMV infectedmice were administered αPD-L1, αCTLA-4, or both for 14 days and ASC inthe spleen was enumerated by ELISPOT. Line represents geometric meanwithin treatment group.

FIGS. 19A-19B are plots showing enhanced B cell and CD4 T cellproliferation and germinal center activity in αPD-L1 treated mice. FIG.19A is a plot of flow cytometric analysis of CD4 T cells and B cellsshows elevated Ki-67 levels following αPD-L1 treatment. Results aregated on either CD4 or B cells as listed above each column FIG. 19B is aset of plots showing an increased frequency of B cells expressing PNAand high levels of FAS, which indicate enhanced germinal center activityin mice treated with αPD-L1. Plots are one representative graphsummarizing the results of two separate experiments.

FIGS. 20A-20C are plots and graphs showing PD-1 expression on CD8 andCD4 T cell subsets. FIG. 20A is a series of images of a flow cytometryexperiment showing co-expression of PD-1 and various phenotypic markersamong CD8+/CD3+ lymphocytes in blood. FIG. 20B is a set of plots of thepercentage of various CD8+/CD3+ and (D) CD4+/CD3+ T cell subsets thatexpress PD-1. Horizontal bars indicate mean percentage of PD-1 on Tcells that are positive (hollow circles) and negative (solid triangles)for the indicated marker. FIG. 20C is a set of plots representing thephenotypic data pf PD-1 expressing CD4+ T cells from one subject.

FIGS. 21A-21B are plots and graphs demonstrating that PD-1 is morehighly expressed among CD8 T cells specific for chronic infections. FIG.21A is a series of images of a flow cytometry experiment showingrepresentative PD-1 staining of Ebstein Bar Virus (EBV), Cylomegalovirus(CMV), influenza and vaccinia virus-specific CD8 T cells. Geometric meanfluorescence intensity (GMFI) of PD-1 expression among tetramer+ cellsis indicated. FIG. 21B is a plot showing a summary of PD-1 GMFI on EBV,CMV, influenza and vaccinia virus-specific CD8 T cells from healthyvolunteers (n=35).

FIGS. 22A-22C are plots and graphs demonstrating that anti-PD-L1blockade increases in vitro proliferation of CD8 T cells specific forchronic infections. FIG. 22A is a series of images of a flow cytometryexperiment showing lymphocytes that were labeled with CFSE, thencultured for 6 days under the indicated conditions. The images showrepresentative staining from EBV and CMV positive subjects. FIG. 22B isa bar graph of EBV, CMV, influenza and vaccinia virus antigen-specificresponses following blockade with anti-PD-L1 blocking antibody. The barsindicate fold increase of tetramer⁺ cells in the presence of peptideplus anti-PD-L1 blocking antibody compared to peptide alone. FIG. 22C isa line graph showing the relationship between the fold-increase intetramer⁺ cells following anti-PD-L1 antibody blockade and PD-1expression (prior to culture).

FIGS. 23A-23C are plots and graphs showing hepatitis C virus (HCV)specific CD8+ T cells express PD-1 in human chronic HCV infection. FIG.23A are representative plots from five patients with chronic HCVinfection showing the expression of PD-1 on HCV specific CD8+ T cells.Numbers in bold identify the frequency of PD-1 expression (x-axis) onHCV specific CD8+ T cells (y-axis). Numbers in italics within the plotsidentify the frequency of tetramer positive cells among total CD8+ Tcells. On the y-axis, 1073 and 1406, identify the HCV epitopespecificity of the tetramer. Patients are identified by “Pt” followed bythe patient number. Cells were gated on CD8+ lymphocytes. Plots are on alogarithmic scale. FIG. 23B is a comparison of PD-1 expression on CD8+ Tcells from healthy donors (CD8 Healthy), HCV infected patients (CD8 HCV)and on CD8+ HCV specific T cells (HCV tet+). FIG. 23C is a graph of PD-1expression on CD8+ T cells specific for influenza virus (Flu tet+) fromHCV infected (HCV+) and healthy donors (Healthy) compared with PD-1expression on CD8+ T cells specific for HCV (HCV tet+). An unpaired ttest was used to compare differences in expression of PD-1 within thesame patient on total CD8+ T cells versus HCV specific CD8+ T cells.

FIGS. 24A-24D are plots and graphs showing the frequency of PD-1expressing CD8+ T cells from the liver is greater than in the peripheralblood. FIG. 24A is representative plots from five patients with chronicHCV infection showing the expression of PD-1 on total CD8+ T cells fromthe peripheral blood versus the liver. Numbers in bold within the plotsidentify the frequency of cells with PD-1 expression among total CD8+ Tcells in the lymphocyte gate. Plots are on a logarithmic scale. FIG. 24Bis a comparison of PD-1 expression on CD8+ T cells from peripheral bloodversus liver in HCV chronically infected patients. A paired t test wasused to compare the difference in PD-1 expression within the samepatients. FIG. 24C is a comparison of PD-1 expression on the CD8+Effector Memory (T_(EM)) cells from peripheral blood versus the liver.Memory subsets were identified by differential expression of CD62L andCD45RA. Bold numbers in the top plots represent the frequency of cellsin each quadrant. Cells were gated on CD8+ lymphocytes. The T_(EM)subset was gated (boxes) and the expression of PD-1 is shown in thehistogram plots below. The dotted line shows PD-1 expression on naïveCD8+ T cells (used as the negative population). The numbers in thehistogram plots represent the frequency of cells expressing PD-1.Comparison of the frequency of PD-1 expression on CD8+ T_(EM) cells forten patients with chronic HCV infection is summarized below thehistogram plots. A paired t test was used to compare the difference inPD-1 expression on CD8+ T_(EM) from the peripheral blood versus theliver within the same patient. FIG. 24D are representative plots fromtwo patients with chronic HCV infection showing the difference in CD127expression on total CD8+ T cells from the peripheral blood versus theliver. Numbers in bold identify the frequency of CD127 expression ontotal CD8+ T cells. Cells were gated on CD8+ lymphocytes. Plots are on alogarithmic scale. A summary of the comparison of CD127 expression ontotal CD8+ T cells in the peripheral blood versus the liver is shownbelow the FACS plots. A paired t test was used for statistical analysis.

FIG. 25 is sets of graphs and plots showing HCV specific CD8+ T cells inthe liver express an exhausted phenotype. Representative plots of PD-1and CD127 expression on HCV specific CD8+ T cells from the peripheralblood and the liver of two patients with chronic HCV infection. Thefirst row of plots identifies the HCV tetramer positive population(boxes). The numbers above the boxes represent the frequency of tetramerpositive cells among CD3+ lymphocytes. The epitope specificity of theHCV tetramer is identified on the y-axis (1073). The second and thirdrow of plots shows PD-1 and CD127 expression on HCV specific CD8+ Tcells from the peripheral blood and liver of two patients with chronicHCV infection. Numbers in bold represent the frequency of PD-1 or CD127expression on HCV specific CD8+ T cells. Plots are on a logarithmicscale and gated on CD3+ CD8+ lymphocytes. Below the FACS plots, asummary of the comparison of PD-1 expression (left) and CD127 expression(right) on total CD8+ T cells versus CD8+ HCV specific T cells from theperiphery (HCV tet+ PBMC) versus HCV specific CD8+ T cells from theliver (HCV tet+ Liver) is shown. Paired t tests were used to compareexpression within the same patient.

FIG. 26 is a set of plots showing blockade of the PD-1/PD-L1 pathwayincreases the expansion of antigen stimulated HCV-specific T cells. CFSElabeled PBMCs from two separate HLA-A2 patients were stimulated usingthe cognate peptide antigen for 6 days in the presence of IL-2 andanti-PD-L1 antibody (top panel) or anti-PD-1 antibody (lower panel). Anunstimulated control is also shown. The percentage of proliferating CFSElow- and CFSE high-HCV-specific HLA-A2+ CD8+ T cells are shown in eachquadrant.

FIGS. 27A-27D are plots and graphs showing elevated PD-1 expression onsimian immunodeficiency virus (SIV) specific CD8 T cells followingSIV239 infection. FIG. 27A is a plot showing PD-1 expression on totalCD8 T cells from a normal macaque. FIG. 27B is a plot showing PD-1expression on total and SIV gag-specific CD8 T cells in a SIV239infected macaque. Analysis was done on PBMC at 12 weeks followingSIV-infection. FIG. 27C is a graph providing a summary of PD-1 positivecells on total and SIV-specific CD8 T cells from normal and SIV-infectedmacaques. Data for SIV-infected macaques represent at 12 weeks followinginfection. FIG. 27D (last panel) is a graph providing a summary of meanfluorescence intensity (MFI) of PD-1 expression on total andSIV-specific CD8 T cells from normal and SIV-infected macaques.

FIGS. 28A-28B are a plot and a graph, respectively, showing in vitroblockade of PD-1 results in enhanced expansion of SIV-specific CD8 Tcells. PBMC from Mamu A*01 positive macaques that were infected withSHIV89.6P were stimulated with P11C peptide (0.1 μg/ml) in the absenceand presence of anti-PD-1 blocking Ab (10 μg/ml) for six days. Afterthree days of stimulation, IL-2 (50 units/ml) was added. At the end ofstimulation cells were stained on the surface for CD3, CD8 and Gag-CM9tetramer. Unstimulated cells (nostim) served as negative controls. Cellswere gated on lymphocytes based on scatter then on CD3 and analyzed forthe expression of CD8 and tetramer. FIG. 28A is a representative FACSplots. Numbers on the graph represent the frequency of tetramer positivecells as a percent of total CD8 T cells. FIG. 28B is a graph providing asummary of data from six macaques. Analyses were performed using cellsobtained at 12 weeks following infection. Fold increase was calculatedas a ratio of the frequency of tetramer positive cells in P11Cstimulated cultures and unstimulated cells.

FIG. 29 is a set of plots showing the kinetics of PD-L1, PD-L2, and PD-1expression on different cell types after LCMV infection. Mice wereinfected with 2×10⁶ pfu of clone-13 (CL-13). PD-L1, PD-L2, and PD-1expression on different type of cells was shown as a histogram at theindicated time points post-infection. Mean fluorescence intensity (MFI)of PD-1 expression on the indicated type of cells is shown.

FIGS. 30A-30C are FACS plots showing in vivo PD-1 blockade duringchronic SIV infection increases the Gag-CM9-specific CD8 T cells withimproved functional quality in both blood and gut. FIG. 30A is arepresentative FACS plots for macaque RRk10. FIGS. 30B and 30C are FACSplots showing the magnitude and phenotype of Gag-CM9-tetramer-positiveCD8 T cells in blood (FIG. 30B) and gut (colorectal mucosal tissue)(FIG. 30 c). Representative FACS plots are shown on the left and summaryfor all Mamu A*01-positive animals is shown on the right. Numbers on theFACS plots represent the frequency of tetramer-positive cells as a percent of total CD8 T cells. Arrows and vertical lines indicate anti-PD-1antibody or control antibody treatment.

FIGS. 31A-31B show that in vivo PD-1 blockade during chronic SIVinfection increases the polyfunctional virus-specific CD8 T cells. FIG.31 a shows the frequency of Gag-specific cytokine-secreting CD8 T cellsas a percentage of total CD8 T cells. Representative FACS plots areshown on the left and summary for the group is shown on the right.Arrows and vertical lines indicate anti-PD-1 antibody or controlantibody treatment. Lines represent anti-PD-1-antibody-treated macaquesand red lines represent control-antibody-treated macaques. FIG. 31Bshows cytokine co-expression subsets expressed as a percentage of totalcytokine-positive cells. Mean percentages for each group are shown.

FIGS. 32A-32C show that in vivo PD-1 blockade during chronic SIVinfection enhances SIV-specific humoral immunity. FIG. 32A showsexpression of PD-1 on memory (CD20⁺CD27⁺CD21⁻) and naïve(CD20⁺CD27⁻CD21⁺) B cells in blood after SIV infection and before invivo PD-1 blockade. FIG. 32B shows titres of anti-SIV Env-bindingantibody in serum after blockade. FIG. 32C shows Ki67 expression (markerfor proliferation) on memory and naïve B cells after blockade. Numberson the FACS plots represent Ki67-positive cells as a percentage ofrespective total cells. Macaques RAf11 and RJd11 were treatedsimultaneously with anti-PD-1 antibody and anti-retroviral therapy at 22weeks after SIV infection.

FIGS. 33A-33E show that in vivo PD-1 blockade reduces plasma viraemiaand prolongs survival of SIV-infected macaques. Plasma viral load inmacaques treated with anti-PD-1 antibody during the early chronic phaseof infection (FIG. 33A), macaques treated with anti-PD-1 antibody duringthe late chronic phase of infection (FIG. 33B), and macaques treatedwith control antibody during the early/late chronic phase of SIVinfection (FIG. 33C). An asterisk indicates death of animal. FIG. 33Dshows the fold reduction in plasma viral load between day 0 and day 28(early chronic study) or day 0 and day 21 (late chronic study). FIG. 33Eshows the survival of SIV-infected macaques after PD-1 blockade.

SEQUENCE LISTING

The nucleic and amino acid sequences listed in the accompanying sequencelisting are shown using standard letter abbreviations for nucleotidebases, and three letter code for amino acids, as defined in 37 C.F.R.1.822. Only one strand of each nucleic acid sequence is shown, but thecomplementary strand is understood as included by any reference to thedisplayed strand. The Sequence Listing is submitted as an ASCII textfile [6975_(—)76374-61_Sequence_Lisiting, Mar. 6, 2015, 23.2 kb], whichis incorporated by reference herein.

In the accompanying sequence listing:

SEQ ID NO: 1 is an exemplary amino acid sequence of human PD-1.

SEQ ID NO: 2 is an exemplary amino acid sequence of mouse PD-1.

SEQ ID NO: 3 is an exemplary amino acid sequence of human PD-L1.

SEQ ID NO: 4 is an exemplary amino acid sequence of human PD-L2.

SEQ ID NOs: 5-12 are exemplary amino acid sequences of human frameworkregions.

SEQ ID NOs: 13-35 are exemplary amino acid sequences of antigenicpeptides.

SEQ ID NOs: 36-43 are the amino acid sequences of majorhistocompatibility peptides.

SEQ ID NO: 44 and SEQ ID NO: 45 are the amino acid sequence of T cellepitopes.

SEQ ID NO: 46 is an exemplary amino acid sequence of a variant humanPD-L2.

SEQ ID NOs: 47-52 are exemplary amino acid sequences of antigenicpeptides.

SEQ ID NOs: 53-56 are the nucleic acid sequences of primers.

DETAILED DESCRIPTION

This disclosure relates to the use of PD-1 antagonists for the inductionof an immune response, such as to a tumor or a persistent viralinfection. This disclosure also relates to methods for determining thedose of a PD-1 antagonist that is effective for treating a subject.

Terms

Unless otherwise noted, technical terms are used according toconventional usage. Definitions of common terms in molecular biology maybe found in Benjamin Lewin, Genes V, published by Oxford UniversityPress, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), TheEncyclopedia of Molecular Biology, published by Blackwell Science Ltd.,1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biologyand Biotechnology: a Comprehensive Desk Reference, published by VCHPublishers, Inc., 1995 (ISBN 1-56081-569-8).

In order to facilitate review of the various embodiments of thisdisclosure, the following explanations of specific terms are provided:

Altering: A statistically significant change in a parameter as comparedto a control value for that parameter. In one example, an “increase” isa statistically significant elevation in a parameter, such as the numberor proliferation of memory B cells, as compared to a control. Suitablestatistical analyses are well known in the art, and include, but are notlimited to, Student's T test and ANOVA assays. In some examples, this isa p value ≦0.05. In other examples, a significant alteration, such as anincrease or a decrease is a change that is two standard deviations fromthe mean or greater. An “absence of a significant alteration” means thata change in a value did not achieve statistical significance, using theappropriate statistical test. In some examples, this is a p value >0.05.In other examples, an “absence of a significant alteration” is anincrease or a decrease that is less than two standard deviations fromthe mean. In some embodiments, an “increase” or “elevation,” such as inthe proliferation of memory B cells, is about a 20%, 30%, 40% 50%, 60%,70%, 80%, 90% or a 2-fold, 3-fold, 4-fold or 5-fold increase. In oneexample, a “decrease” or “reduction” is a statistically significantdecline in a parameter, such as the number or proliferation of memory Bcells, as compared to a control. Suitable statistical analyses are wellknown in the art, and include, but are not limited to, Student's T testand ANOVA assays. In some embodiments, a “decrease,” such as in theproliferation of memory B cells, is about a 20%, 30%, 40% 50%, 60%, 70%,80%, 90% or a 2-fold, 3-fold, 4-fold or 5-fold decrease.

Antisense, Sense, and Antigene:

DNA has two antiparallel strands, a 5′→3′ strand, referred to as theplus strand, and a 3′→5′ strand, referred to as the minus strand.Because RNA polymerase adds nucleic acids in a 5′→3′ direction, theminus strand of the DNA serves as the template for the RNA duringtranscription. Thus, an RNA transcript will have a sequencecomplementary to the minus strand, and identical to the plus strand(except that U is substituted for T).

Antisense molecules are molecules that are specifically hybridizable orspecifically complementary to either RNA or the plus strand of DNA.Sense molecules are molecules that are specifically hybridizable orspecifically complementary to the minus strand of DNA. Antigenemolecules are either antisense or sense molecules directed to a DNAtarget. An antisense RNA (asRNA) is a molecule of RNA complementary to asense (encoding) nucleic acid molecule.

Amplification: When used in reference to a nucleic acid, this refers totechniques that increase the number of copies of a nucleic acid moleculein a sample or specimen. An example of amplification is the polymerasechain reaction, in which a biological sample collected from a subject iscontacted with a pair of oligonucleotide primers, under conditions thatallow for the hybridization of the primers to nucleic acid template inthe sample. The primers are extended under suitable conditions,dissociated from the template, and then re-annealed, extended, anddissociated to amplify the number of copies of the nucleic acid. Theproduct of in vitro amplification can be characterized byelectrophoresis, restriction endonuclease cleavage patterns,oligonucleotide hybridization or ligation, and/or nucleic acidsequencing, using standard techniques. Other examples of in vitroamplification techniques include strand displacement amplification (seeU.S. Pat. No. 5,744,311); transcription-free isothermal amplification(see U.S. Pat. No. 6,033,881); repair chain reaction amplification (seeWO 90/01069); ligase chain reaction amplification (see EP-A-320 308);gap filling ligase chain reaction amplification (see U.S. Pat. No.5,427,930); coupled ligase detection and PCR (see U.S. Pat. No.6,027,889); and NASBA™ RNA transcription-free amplification (see U.S.Pat. No. 6,025,134).

Antibody: A polypeptide ligand comprising at least a light chain orheavy chain immunoglobulin variable region which specifically recognizesand binds an epitope (e.g., an antigen, such as a tumor or viral antigenor a fragment thereof). This includes intact immunoglobulins and thevariants and portions of them well known in the art, such as Fab′fragments, F(ab)′2 fragments, single chain Fv proteins (“scFv”), anddisulfide stabilized Fv proteins (“dsFv”). A scFv protein is a fusionprotein in which a light chain variable region of an immunoglobulin anda heavy chain variable region of an immunoglobulin are bound by alinker, while in dsFvs, the chains have been mutated to introduce adisulfide bond to stabilize the association of the chains. The term alsoincludes genetically engineered forms such as chimeric antibodies (e.g.,humanized murine antibodies), heteroconjugate antibodies (e.g.,bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995(Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology, 3^(rd) Ed.,W.H. Freeman & Co., New York, 1997.

Typically, an immunoglobulin has a heavy and light chain. Each heavy andlight chain contains a constant region and a variable region, (theregions are also known as “domains”). In combination, the heavy and thelight chain variable regions specifically bind the antigen. Light andheavy chain variable regions contain a “framework” region interrupted bythree hypervariable regions, also called “complementarity-determiningregions” or “CDRs”. The extent of the framework region and CDRs has beendefined (see, Kabat et al., Sequences of Proteins of ImmunologicalInterest, U.S. Department of Health and Human Services, 1991, which ishereby incorporated by reference). The Kabat database is now maintainedonline. The sequences of the framework regions of different light orheavy chains are relatively conserved within a species. The frameworkregion of an antibody, that is the combined framework regions of theconstituent light and heavy chains, serves to position and align theCDRs in three-dimensional space.

The CDRs are primarily responsible for binding to an epitope of anantigen. The CDRs of each chain are typically referred to as CDR1, CDR2,and CDR3, numbered sequentially starting from the N-terminus, and arealso typically identified by the chain in which the particular CDR islocated. Thus, a V_(H) CDR3 is located in the variable domain of theheavy chain of the antibody in which it is found, whereas a V_(L) CDR1is the CDR1 from the variable domain of the light chain of the antibodyin which it is found.

References to “V_(H)” or “VH” refer to the variable region of animmunoglobulin heavy chain, including that of an Fv, scFv, dsFv or Fab.References to “V_(L)” or “VL” refer to the variable region of animmunoglobulin light chain, including that of an Fv, scFv, dsFv or Fab.

A “monoclonal antibody” is an antibody produced by a single clone ofB-lymphocytes or by a cell into which the light and heavy chain genes ofa single antibody have been transfected. Monoclonal antibodies areproduced by methods known to those of skill in the art, for instance bymaking hybrid antibody-forming cells from a fusion of myeloma cells withimmune spleen cells. Monoclonal antibodies include humanized monoclonalantibodies.

A “humanized” immunoglobulin is an immunoglobulin including a humanframework region and one or more CDRs from a non-human (such as a mouse,rat, or synthetic) immunoglobulin. The non-human immunoglobulinproviding the CDRs is termed a “donor,” and the human immunoglobulinproviding the framework is termed an “acceptor.” In one embodiment, allthe CDRs are from the donor immunoglobulin in a humanizedimmunoglobulin. Constant regions need not be present, but if they are,they must be substantially identical to human immunoglobulin constantregions, i.e., at least about 85-90%, such as about 95% or moreidentical. Hence, all parts of a humanized immunoglobulin, exceptpossibly the CDRs, are substantially identical to corresponding parts ofnatural human immunoglobulin sequences. A “humanized antibody” is anantibody comprising a humanized light chain and a humanized heavy chainimmunoglobulin. A humanized antibody binds to the same antigen as thedonor antibody that provides the CDRs. The acceptor framework of ahumanized immunoglobulin or antibody may have a limited number ofsubstitutions by amino acids taken from the donor framework. Humanizedor other monoclonal antibodies can have additional conservative aminoacid substitutions which have substantially no effect on antigen bindingor other immunoglobulin functions. Humanized immunoglobulins can beconstructed by means of genetic engineering (e.g., see U.S. Pat. No.5,585,089).

A “neutralizing antibody” is an antibody that interferes with any of thebiological activities of a polypeptide, such as a PD-1 polypeptide. Forexample, a neutralizing antibody can interfere with the ability of aPD-1 polypeptide to reduce an immune response such as the cytotoxicityof T cells. In several examples, the neutralizing antibody can reducethe ability of a PD-1 polypeptide to reduce an immune response by about50%, about 70%, about 90% or more. Any standard assay to measure immuneresponses, including those described herein, may be used to assesspotentially neutralizing antibodies.

Antigen: A compound, composition, or substance that can stimulate theproduction of antibodies or a T cell response in an animal, includingcompositions that are injected or absorbed into an animal. An antigenreacts with the products of specific humoral or cellular immunity,including those induced by heterologous immunogens. The term “antigen”includes all related antigenic epitopes. “Epitope” or “antigenicdeterminant” refers to a site on an antigen to which B and/or T cellsrespond. In one embodiment, T cells respond to the epitope, when theepitope is presented in conjunction with an MHC molecule. Epitopes canbe formed both from contiguous amino acids or noncontiguous amino acidsjuxtaposed by tertiary folding of a protein. Epitopes formed fromcontiguous amino acids are typically retained on exposure to denaturingsolvents whereas epitopes formed by tertiary folding are typically loston treatment with denaturing solvents. An epitope typically includes atleast 3, and more usually, at least 5, about 9, or about 8-10 aminoacids in a unique spatial conformation. Methods of determining spatialconformation of epitopes include, for example, x-ray crystallography and2-dimensional nuclear magnetic resonance.

An antigen can be a tissue-specific antigen, or a disease-specificantigen. These terms are not exclusive, as a tissue-specific antigen canalso be a disease specific antigen. A tissue-specific antigen isexpressed in a limited number of tissues, such as a single tissue.Specific, non-limiting examples of a tissue specific antigen are aprostate specific antigen, a uterine specific antigen, and/or a testesspecific antigen. A tissue specific antigen may be expressed by morethan one tissue, such as, but not limited to, an antigen that isexpressed in more than one reproductive tissue, such as in both prostateand uterine tissue. A disease-specific antigen is expressedcoincidentally with a disease process. Specific non-limiting examples ofa disease-specific antigen are an antigen whose expression correlateswith, or is predictive of, tumor formation. A disease-specific antigencan be an antigen recognized by T cells or B cells.

Antigen-presenting cell (APC): A cell that can present antigen bound toMHC class I or class II molcules to T cells. APCs include, but are notlimited to, monocytes, macrophages, dendritic cells, B cells, T cellsand Langerhans cells. A T cell that can present antigen to other T cells(including CD4+ and/or CD8+ T cells) is an antigen presenting T cell(T-APC).

B Cells: A subset of lymphocytes, that is, white blood cells(leukocytes). Mature B cells differentiate into plasma cells, whichproduces antibodies, and memory B cells. A “B cell progenitor” is a cellthat can develop into a mature B cell. B cell progenitors include stemcells, early pro-B cells, late pro-B cells, large pre-B cells, smallpre-B cells, and immature B cells and transitional B cells. Generally,early pro-B cells (that express, for example, CD43 or B220) undergoimmunoglobulin heavy chain rearrangement to become late pro B and pre Bcells, and further undergo immunoglobulin light chain rearrangement tobecome an immature B cells. Immature B cells include T1 and T2 B cells.For example, in mice, immature B cells include T1 B cells that areAA41^(hi)CD23^(lo) cells. Another example of a mouse immature B cell isa T2 B that is an AA41^(hi)CD23^(hi) cell. In humans, immature B cells(for example, immature peripheral transitional B cells) includeCD38^(hi), IgD⁺, CD10⁺, CD24^(hi), CD44^(lo), CD23^(lo) and CD1^(lo)cells. Thus, immature B cells include B220 (CD45R) expressing cellswherein the light and the heavy chain immunoglobulin genes arerearranged. In one embodiment, immature B cells express CD45R, class II,IgM, CD19 and CD40. Immature B cells do not exhibit surrogate lightchain expression, but do express Ig αβ and RAG Immature B cells candevelop into mature B cells, which can produce immunoglobulins (e.g.,IgA, IgG or IgM). Mature B cells have acquired surface IgM and IgD, arecapable of responding to antigen, and express characteristic markerssuch as CD21 and CD23 (CD23^(hi)CD21^(hi) cells). B cells can beactivated by agents such as lippopolysaccharide (LPS) or IL-4 andantibodies to IgM. Common biological sources of B cells and B cellprogenitors include bone marrow, peripheral blood, spleen and lymphnodes.

B cells that encounter antigen for the first time are known as “naïve” Bcells; the cells have IgM and IgD on their cell surfaces. After a B cellprogenitor (e.g., a pre-committed small lymphocyte) is stimulated by anantigen, it differentiates into a blast cell, which differentiates intoan immature plasma cell that can differentiate into either a matureplasma cell or a memory B cell. A mature plasma cell secretesimmunoglobulins in response to a specific antigen. A memory B cell is aB cell that undergoes isotype switching and somatic hypermutation thatis generally found during a secondary immune response (a subsequentantigen exposure following a primary exposure) but can also be detectedduring a primary antigen response. The development of memory B cellstakes place in germinal centers (GC) of lymphoid follicles whereantigen-driven lymphocytes undergo somatic hypermutation and affinityselection, presumably under the influence of helper T cells. Memory Bcells generally express CD27. Typically, memory B cells also expresshigh affinity antigen specific immunoglobulin (B cell receptor) on theircell surface. Thus, memory B cells can be CD20⁺CD27⁺, and includeCD20^(int)/CD21⁺/CD27⁺ (resting memory), CD20^(hi)/CD21⁻/CD27⁺(activated memory). CD20^(hi)/CD21⁻/CD27⁻ cells are distinct“unconventional or tissue memory” B cells.

Binding affinity: Affinity of an antibody for an antigen. In oneembodiment, affinity is calculated by a modification of the Scatchardmethod described by Frankel et al., Mol. Immunol., 16:101-106, 1979. Inanother embodiment, binding affinity is measured by an antigen/antibodydissociation rate. In yet another embodiment, a high binding affinity ismeasured by a competition radioimmunoassay. In several examples, a highbinding affinity is at least about 1×10⁻⁸ M. In other embodiments, ahigh binding affinity is at least about 1.5×10⁻⁸, at least about2.0×10⁻⁸, at least about 2.5×10⁻⁸, at least about 3.0×10⁻⁸, at leastabout 3.5×10⁻⁸, at least about 4.0×10⁻⁸, at least about 4.5×10⁻⁸, or atleast about 5.0×10⁻⁸ M.

Binding or stable binding (oligonucleotide): An oligonucleotide binds orstably binds to a target nucleic acid if a sufficient amount of theoligonucleotide forms base pairs or is hybridized to its target nucleicacid, to permit detection of that binding. Binding can be detected byeither physical or functional properties of the target: oligonucleotidecomplex. Binding between a target and an oligonucleotide can be detectedby any procedure known to one skilled in the art, including bothfunctional and physical binding assays. For instance, binding can bedetected functionally by determining whether binding has an observableeffect upon a biosynthetic process such as expression of a gene, DNAreplication, transcription, translation and the like.

Physical methods of detecting the binding of complementary strands ofDNA or RNA are well known in the art, and include such methods as DNaseI or chemical footprinting, gel shift and affinity cleavage assays,Northern blotting, dot blotting and light absorption detectionprocedures. For example, one method that is widely used, because it issimple and reliable, involves observing a change in light absorption ofa solution containing an oligonucleotide (or an analog) and a targetnucleic acid at 220 to 300 nm as the temperature is slowly increased. Ifthe oligonucleotide or analog has bound to its target, there is a suddenincrease in absorption at a characteristic temperature as theoligonucleotide (or analog) and the target disassociate from each other,or melt.

The binding between an oligomer and its target nucleic acid isfrequently characterized by the temperature (T_(m)) at which 50% of theoligomer is melted from its target. A higher (T_(m)) means a stronger ormore stable complex relative to a complex with a lower (T_(m)).

Cancer or Tumor: A malignant neoplasm that has undergone characteristicanaplasia with loss of differentiation, increase rate of growth,invasion of surrounding tissue, and is capable of metastasis. Areproductive cancer is a cancer that has its primary origin in areproductive tissue, such as in the uterus, testes, ovary, prostate,fallopian tube, or penis. For example, prostate cancer is a malignantneoplasm that arises in or from prostate tissue, and uterine cancer is amalignant neoplasm that arises in or from uterine tissue, and testicularcancer is a malignant neoplasm that arises in the testes. Residualcancer is cancer that remains in a subject after any form of treatmentgiven to the subject to reduce or eradicate thyroid cancer. Metastaticcancer is a cancer at one or more sites in the body other than the siteof origin of the original (primary) cancer from which the metastaticcancer is derived.

CD28 (Cluster of Differentiation 28): One of the molecules expressed onT cells that provide co-stimulatory signals, which are required for Tcell activation. CD28 is the receptor for B7.1 (CD80) and B7.2 (CD86).When activated by Toll-like receptor ligands, the B7.1 expression isupregulated in antigen presenting cells (APCs). The B7.2 expression onantigen presenting cells is constitutive. CD28 is the only B7 receptorconstitutively expressed on naïve T cells.

Chemotherapy; chemotherapeutic agents: As used herein, any chemicalagent with therapeutic usefulness in the treatment of diseasescharacterized by abnormal cell growth. Such diseases include tumors,neoplasms and cancer as well as diseases characterized by hyperplasticgrowth such as psoriasis. In one embodiment, a chemotherapeutic agent isan agent of use in treating neoplasms such as solid tumors. In oneembodiment, a chemotherapeutic agent is a radioactive molecule. One ofskill in the art can readily identify a chemotherapeutic agent of use(e.g. see Slapak and Kufe, Principles of Cancer Therapy, Chapter 86 inHarrison's Principles of Internal Medicine, 14th edition; Perry et al.,Chemotherapy, Ch. 17 in Abeloff, Clinical Oncology 2nd ed., © 2000Churchill Livingstone, Inc; Baltzer L, Berkery R (eds): Oncology PocketGuide to Chemotherapy, 2nd ed. St. Louis, Mosby-Year Book, 1995; FischerD S, Knobf M F, Durivage H J (eds): The Cancer Chemotherapy Handbook,4th ed. St. Louis, Mosby-Year Book, 1993). The immunogenic polypeptidesdisclosed herein can be used in conjunction with additionalchemotherapeutic agents.

CD28: A cell surface antigen is known also as T90/44 antigen or Tp44that is expressed on T cells. CD28 is a receptor for co-stimulatoryproteins acting on T-cells. The natural ligand of CD28 is a 44-54 kDaglycoprotein, called B7-1 or CD80. There is a related molecule, B7-2.B7-1 is expressed on activated B cells and other antigen-presentingcells. It is expressed by macrophages, keratinocytes, T-cells, B-cells,peripheral blood dendritic and Langerhans cells. B7-2 is found on blooddendritic and Langerhans cells, B-cells, macrophages, Kupffer cells,activated monocytes and various natural killer cell clones. Binding ofB7 to CD28 on T-cells delivers a costimulatory signal that triggersT-cell proliferation

Control level (immune parameter): A baseline level of an immuneparameter. In some embodiments, and control level is the level of acomponent of the immune system, such as memory B cells or proliferatingmemory B cells, in the absence of a therapeutic agent. A control levelcan be measured in a sample from a subject that has not been treatedwith an agent of interest, or a sample from a subject that has beentreated with a control agent. The control level can also be a standardvalue, such as a value determined from an average of a large number ofsamples over time. The control level can also be measured in a samplefrom a subject treated with the specific dose of a therapeutic agent,wherein that dose is not administered to the subject at the time thesubject is currently under evaluation. The control can be from thesubject under evaluation, or can be from a different subject.

Control level (polypeptide or nucleic acid): The level of a molecule,such as a polypeptide or nucleic acid, normally found in nature under acertain condition and/or in a specific genetic background. In certainembodiments, a control level of a molecule can be measured in a cell orspecimen that has not been subjected, either directly or indirectly, toa treatment. In some examples, a control level can be the level in acell not contacted with the agent, such as a PD-1 antagonist. Inadditional examples, a control level can be the level in a subject notadministered the PD-1 antagonist.

DNA (deoxyribonucleic acid): DNA is a long chain polymer which comprisesthe genetic material of most living organisms (some viruses have genescomprising ribonucleic acid (RNA)). The repeating units in DNA polymersare four different nucleotides, each of which comprises one of the fourbases, adenine, guanine, cytosine and thymine bound to a deoxyribosesugar to which a phosphate group is attached. Triplets of nucleotides(referred to as codons) code for each amino acid in a polypeptide, orfor a stop signal. The term codon is also used for the corresponding(and complementary) sequences of three nucleotides in the mRNA intowhich the DNA sequence is transcribed.

Unless otherwise specified, any reference to a DNA molecule is intendedto include the reverse complement of that DNA molecule. Except wheresingle-strandedness is required by the text herein, DNA molecules,though written to depict only a single strand, encompass both strands ofa double-stranded DNA molecule.

Detecting or detection (cell or biomolecule): Refers to quantitativelyor qualitatively determining the presence of a biomolecule or specificcell type, such as a memory B cell, under investigation. For example,quantitatively or qualitatively determining the presence of memory Bcells in a sample from a subject, or detecting proliferating memory Bcells. Generally, detection of a biological molecule, such as a protein,nucleic acid, or detecting a specific cell type or cell proliferation,requires performing a biological assay and not simple observation. Forexample, assays that utilize antibodies or nucleic acid probes (whichcan both be labeled), or can be used to detect proteins or cells,respectively. Diagnosing or diagnosis of the efficacy of treatment witha PD-1 antagonist involves detecting a significant change in a cell orbiomolecule, such as the proliferation of memory B cells.

Encode: A polynucleotide is said to encode a polypeptide if, in itsnative state or when manipulated by methods well known to those skilledin the art, it can be transcribed and/or translated to produce the mRNAfor and/or the polypeptide or a fragment thereof. The anti-sense strandis the complement of such a nucleic acid, and the encoding sequence canbe deduced therefrom.

Expression: The process by which a gene's coded information is convertedinto the structures present and operating in the cell. Expressed genesinclude those that are transcribed into mRNA and then translated intoprotein and those that are transcribed into RNA but not translated intoprotein (for example, siRNA, transfer RNA and ribosomal RNA). Thus,expression of a target sequence, such as a gene or a promoter region ofa gene, can result in the expression of an mRNA, a protein, or both. Theexpression of the target sequence can be inhibited or enhanced(decreased or increased).

Expression Control Sequences: Nucleic acid sequences that regulate theexpression of a heterologous nucleic acid sequence to which it isoperatively linked. Expression control sequences are operatively linkedto a nucleic acid sequence when the expression control sequences controland regulate the transcription and, as appropriate, translation of thenucleic acid sequence. Thus, expression control sequences can includeappropriate promoters, enhancers, transcription terminators, a startcodon (i.e., ATG) in front of a protein-encoding gene, splicing signals,elements for the maintenance of the correct reading frame of that geneto permit proper translation of mRNA, and stop codons. The term “controlsequences” is intended to include, at a minimum, components whosepresence can influence expression, and can also include additionalcomponents whose presence is advantageous, for example, leader sequencesand fusion partner sequences. Expression control sequences can include apromoter.

A promoter is a minimal sequence sufficient to direct transcription.Also included are those promoter elements which are sufficient to renderpromoter-dependent gene expression controllable for cell-type specific,tissue-specific, or inducible by external signals or agents; suchelements may be located in the 5′ or 3′ regions of the gene. Bothconstitutive and inducible promoters are included (see e.g., Bitter etal., Methods in Enzymology 153:516-544, 1987). For example, when cloningin bacterial systems, inducible promoters such as pL of bacteriophagelambda, plac, pap, ptac (ptrp-lac hybrid promoter) and the like can beused. In one embodiment, when cloning in mammalian cell systems,promoters derived from the genome of mammalian cells (such as themetallothionein promoter) or from mammalian viruses (such as theretrovirus long terminal repeat; the adenovirus late promoter; thevaccinia virus 7.5K promoter) can be used. Promoters produced byrecombinant DNA or synthetic techniques can also be used to provide fortranscription of the nucleic acid sequences.

Heterologous: Originating from separate genetic sources or species.Generally, an antibody that specifically binds to a protein of interestwill not specifically bind to a heterologous protein.

Host cells: Cells in which a vector can be propagated and its DNAexpressed. The cell may be prokaryotic or eukaryotic. The cell can bemammalian, such as a human cell. The term also includes any progeny ofthe subject host cell. It is understood that all progeny may not beidentical to the parental cell since there may be mutations that occurduring replication. However, such progeny are included when the term“host cell” is used.

Immune response: A response of a cell of the immune system, such as a Bcell, T cell, or monocyte, to a stimulus. In one embodiment, theresponse is specific for a particular antigen (an “antigen-specificresponse”). In one embodiment, an immune response is a T cell response,such as a CD4+ response or a CD8+ response. In another embodiment, theresponse is a B cell response, and results in the production of specificantibodies, or the proliferation of memory B cells. A B cell responsecan be a memory B cell response or a plasma B cell response. An exampleof a plasma B cell response is the production of antibody. An example ofa response of a memory B cell is proliferation of memory B cells.

“Unresponsiveness” with regard to immune cells includes refractivity ofimmune cells to stimulation, such as stimulation via an activatingreceptor or a cytokine. Unresponsiveness can occur, for example, becauseof exposure to immunosuppressants or exposure to high doses of antigen.As used herein, the term “anergy” or “tolerance” includes refractivityto activating receptor-mediated stimulation. Such refractivity isgenerally antigen-specific and persists after exposure to the tolerizingantigen has ceased.

For example, anergy in T cells (as opposed to unresponsiveness) ischaracterized by lack of cytokine production (such as IL-2). T cellanergy occurs when T cells are exposed to antigen and receive a firstsignal (a T cell receptor or CD-3 mediated signal) in the absence of asecond signal (a costimulatory signal). Under these conditions,re-exposure of the cells to the same antigen (even if exposure occurs inthe presence of a costimulatory molecule) results in failure to producecytokines and, thus, failure to proliferate. Anergic T cells can,however, mount responses to unrelated antigens and can proliferate ifcultured with cytokines (such as IL-2). For example, T cell anergy canalso be observed by the lack of IL-2 production by T lymphocytes asmeasured by ELISA or by a proliferation assay using an indicator cellline. Alternatively, a reporter gene construct can be used. For example,anergic T cells fail to initiate IL-2 gene transcription induced by aheterologous promoter under the control of the 5′ IL-2 gene enhancer orby a multimer of the AP1 sequence that can be found within the enhancer(Kang et al. Science 257:1134, 1992). Anergic antigen specific T cellsmay have a reduction of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%,90%, 95%, or even 100% in cytotoxic activity relative a correspondingcontrol antigen specific T cell.

Immunogenic peptide: A peptide which comprises an allele-specific motifor other sequence such that the peptide will bind an MHC molecule andinduce a cytotoxic T lymphocyte (“CTL”) response, or a B cell response(e.g. antibody production or memory B cell proliferation) specific tothe antigen from which the immunogenic peptide is derived.

In one embodiment, immunogenic peptides are identified using sequencemotifs or other methods, such as neural net or polynomialdeterminations, known in the art. Typically, algorithms are used todetermine the “binding threshold” of peptides to select those withscores that give them a high probability of binding at a certainaffinity and will be immunogenic. The algorithms are based either on theeffects on MHC binding of a particular amino acid at a particularposition, the effects on antibody binding of a particular amino acid ata particular position, or the effects on binding of a particularsubstitution in a motif-containing peptide. Within the context of animmunogenic peptide, a “conserved residue” is one which appears in asignificantly higher frequency than would be expected by randomdistribution at a particular position in a peptide. In one embodiment, aconserved residue is one where the MHC structure may provide a contactpoint with the immunogenic peptide.

Immunogenic peptides can also be identified by measuring their bindingto a specific MHC protein (e.g. HLA-A02.01) and by their ability tostimulate CD4 and/or CD8 when presented in the context of the MHCprotein.

Immunogenic composition: A composition comprising an immunogenicpolypeptide or a nucleic acid encoding the immunogenic polypeptide thatinduces a measurable CTL response against cells expressing thepolypeptide, or induces a measurable B cell response (such as productionof antibodies that specifically bind the polypeptide or proliferation ofmemory B cells) against the polypeptide. For in vitro use, theimmunogenic composition can consist of the isolated nucleic acid, vectorincluding the nucleic acid/or immunogenic peptide. For in vivo use, theimmunogenic composition will typically comprise the nucleic acid, vectorincluding the nucleic acid, and or immunogenic polypeptide, inpharmaceutically acceptable carriers, and/or other agents. Animmunogenic composition can optionally include an adjuvant, a PD-1antagonist, a costimulatory molecule, or a nucleic acid encoding acostimulatory molecule. A polypeptide, or nucleic acid encoding thepolypeptide, can be readily tested for its ability to induce a CTL byart-recognized assays.

Immunologically reactive conditions (in vitro): Includes “conditionssufficient to form an immune complex” which allow an antibody raisedagainst a particular epitope to bind to that epitope to a detectablygreater degree than, and/or to the substantial exclusion of, binding tosubstantially all other epitopes. Immunologically reactive conditionsare dependent upon the format of the antibody binding reaction andtypically are those utilized in immunoassay protocols (such as ELISA orradioimmunoassay), FACS or those conditions encountered in vivo. SeeHarlow & Lane, Antibodies, A Laboratory Manual, Cold Spring HarborPublications, New York (1988), for a description of immunoassay formatsand conditions. The immunologically reactive conditions employed in themethods disclosed herein are “physiological conditions” which includereference to conditions (e.g., temperature, osmolarity, pH) that aretypical inside a living mammal or a mammalian cell. While it isrecognized that some organs are subject to extreme conditions, theintra-organismal and intracellular environment normally lies around pH 7(i.e., from pH 6.0 to pH 8.0, more typically pH 6.5 to 7.5), containswater as the predominant solvent, and exists at a temperature above 0°C. and below 50° C. Osmolarity is within the range that is supportive ofcell viability and proliferation.

Inhibiting or treating a disease: Inhibiting a disease, such as tumorgrowth or a persistent infection, refers to inhibiting the fulldevelopment of a disease or lessening the physiological effects of thedisease process. In several examples, inhibiting or treating a diseaserefers to lessening symptoms of a tumor or an infection with a pathogen.For example, cancer treatment can prevent the development ofparaneoplastic syndrome in a person who is known to have a cancer, orlessening a sign or symptom of the tumor. In another embodiment,treatment of an infection can refer to inhibiting development orlessening a symptom of the infection. “Treatment” refers to atherapeutic intervention that ameliorates a sign or symptom of a diseaseor pathological condition related to the disease. Therapeuticvaccination refers to administration of an agent to a subject alreadyinfected with a pathogen. The subject can be asymptomatic, so that thetreatment prevents the development of a symptom. The therapeutic vaccinecan also reduce the severity of one or more existing symptoms, or reducepathogen load.

Infectious disease: Any disease caused by an infectious agent. Examplesof infectious pathogens include, but are not limited to: viruses,bacteria, mycoplasma and fungi. In a particular example, it is a diseasecaused by at least one type of infectious pathogen. In another example,it is a disease caused by at least two different types of infectiouspathogens. Infectious diseases can affect any body system, be acute(short-acting) or chronic/persistent (long-acting), occur with orwithout fever, strike any age group, and overlap each other.

Viral diseases commonly occur after immunosupression due tore-activation of viruses already present in the recipient. Particularexamples of persistent viral infections include, but are not limited to,cytomegalovirus (CMV) pneumonia, enteritis and retinitis; Epstein-Barrvirus (EBV) lymphoproliferative disease; chicken pox/shingles (caused byvaricella zoster virus, VZV); HSV-1 and -2 mucositis; HSV-6encephalitis, BK-virus hemorrhagic cystitis; viral influenza; pneumoniafrom respiratory syncytial virus (RSV); AIDS (caused by HIV); andhepatitis A, B or C.

Additional examples of infectious virus include: Retroviridae;Picornaviridae (for example, polio viruses, hepatitis A virus;enteroviruses, human coxsackie viruses, rhinoviruses, echoviruses);Calciviridae (such as strains that cause gastroenteritis); Togaviridae(for example, equine encephalitis viruses, rubella viruses); Flaviridae(for example, dengue viruses, encephalitis viruses, yellow feverviruses); Coronaviridae (for example, coronaviruses); Rhabdoviridae (forexample, vesicular stomatitis viruses, rabies viruses); Filoviridae (forexample, ebola viruses); Paramyxoviridae (for example, parainfluenzaviruses, mumps virus, measles virus, respiratory syncytial virus);Orthomyxoviridae (for example, influenza viruses); Bungaviridae (forexample, Hantaan viruses, bunga viruses, phleboviruses and Nairoviruses); Arena viridae (hemorrhagic fever viruses); Reoviridae (e.g.,reoviruses, orbiviurses and rotaviruses); Birnaviridae; Hepadnaviridae(Hepatitis B virus); Parvoviridae (parvoviruses); Papovaviridae(papilloma viruses, polyoma viruses); Adenoviridae (most adenoviruses);Herpesviridae (herpes simplex virus (HSV) 1 and HSV-2, varicella zostervirus, cytomegalovirus (CMV), herpes viruses); Poxviridae (variolaviruses, vaccinia viruses, pox viruses); and Iridoviridae (such asAfrican swine fever virus); and unclassified viruses (for example, theetiological agents of Spongiform encephalopathies, the agent of deltahepatitis (thought to be a defective satellite of hepatitis B virus),the agents of non-A, non-B hepatitis (class 1=internally transmitted;class 2=parenterally transmitted (i.e., Hepatitis C); Norwalk andrelated viruses, and astroviruses).

Examples of fungal infections include but are not limited to:aspergillosis; thrush (caused by Candida albicans); cryptococcosis(caused by Cryptococcus); and histoplasmosis. Thus, examples ofinfectious fungi include, but are not limited to, Cryptococcusneoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomycesdermatitidis, Chlamydia trachomatis, Candida albicans.

Examples of infectious bacteria include: Helicobacter pyloris, Boreliaburgdorferi, Legionella pneumophilia, Mycobacteria sps (such as. M.tuberculosis, M. avium, M. intracellulare, M. kansaii, M. gordonae),Staphylococcus aureus, Neisseria gonorrhoeae, Neisseria meningitidis,Listeria monocytogenes, Streptococcus pyogenes (Group A Streptococcus),Streptococcus agalactiae (Group B Streptococcus), Streptococcus(viridans group), Streptococcus faecalis, Streptococcus bovis,Streptococcus (anaerobic sps.), Streptococcus pneumoniae, pathogenicCampylobacter sp., Enterococcus sp., Haemophilus influenzae, Bacillusanthracis, corynebacterium diphtheriae, corynebacterium sp.,Erysipelothrix rhusiopathiae, Clostridium perfringers, Clostridiumtetani, Enterobacter aerogenes, Klebsiella pneumoniae, Pasturellamultocida, Bacteroides sp., Fusobacterium nucleatum, Streptobacillusmoniliformis, Treponema pallidium, Treponema pertenue, Leptospira, andActinomyces israelli. Other infectious organisms (such as protists)include: Plasmodium falciparum and Toxoplasma gondii.

A “persistent infection” is an infection in which the infectious agent(such as a virus, mycoplasma, bacterium, parasite, or fungus) is notcleared or eliminated from the infected host, even after the inductionof an immune response. Persistent infections can be chronic infections,latent infections, or slow infections. Latent infection is characterizedby the lack of demonstrable infectious virus between episodes ofrecurrent disease. Chronic infection is characterized by the continuedpresence of infectious virus following the primary infection and caninclude chronic or recurrent disease. Slow infection is characterized bya prolonged incubation period followed by progressive disease. Unlikelatent and chronic infections, slow infection may not begin with anacute period of viral multiplication. While acute infections arerelatively brief (lasting a few days to a few weeks) and resolved fromthe body by the immune system, persistent infections can last forexample, for months, years, or even a lifetime. These infections mayalso recur frequently over a long period of time, involving stages ofsilent and productive infection without cell killing or even producingexcessive damage to the host cells. Persistent infections often involvestages of both silent and productive infection without rapidly killingor even producing excessive damage of the host cells. During persistentviral infections, the viral genome can be either stably integrated intothe cellular DNA or maintained episomally. Persistent infection occurswith viruses such as human T-Cell leukemia viruses, Epstein-Barr virus,cytomegalovirus, herpesviruses, varicella-zoster virus, measles,papovaviruses, prions, hepatitis viruses, adenoviruses, parvoviruses andpapillomaviruses.

The causative infectious agents may also be detected in the host (suchas inside specific cells of infected individuals) even after the immuneresponse has resolved, using standard techniques. Mammals are diagnosedas having a persistent infection according to any standard method knownin the art and described, for example, in U.S. Pat. Nos. 6,368,832,6,579,854, and 6,808,710 and U.S. Patent Application Publication Nos.20040137577, 20030232323, 20030166531, 20030064380, 20030044768,20030039653, 20020164600, 20020160000, 20020110836, 20020107363, and20020106730, all of which are hereby incorporated by reference.

“Alleviating a symptom of a persistent infection” is ameliorating anycondition or symptom associated with the persistent infection.Alternatively, alleviating a symptom of a persistent infection caninvolve reducing the infectious microbial (such as viral, bacterial,fungal or parasitic) load in the subject relative to such load in anuntreated control. As compared with an equivalent untreated control,such reduction or degree of prevention is at least 5%, 10%, 20%, 40%,50%, 60%, 80%, 90%, 95%, or 100% as measured by any standard technique.Desirably, the persistent infection is completely cleared as detected byany standard method known in the art, in which case the persistentinfection is considered to have been treated. A patient who is beingtreated for a persistent infection is one who a medical practitioner hasdiagnosed as having such a condition. Diagnosis may be by any suitablemeans. Diagnosis and monitoring may involve, for example, detecting thelevel of microbial load in a biological sample (for example, a tissuebiopsy, blood test, or urine test), detecting the level of a surrogatemarker of the microbial infection in a biological sample, detectingsymptoms associated with persistent infections, or detecting immunecells involved in the immune response typical of persistent infections(for example, detection of antigen specific T cells that are anergicand/or functionally impaired). A patient in whom the development of apersistent infection is being prevented may or may not have receivedsuch a diagnosis. One in the art will understand that these patients mayhave been subjected to the same standard tests as described above or mayhave been identified, without examination, as one at high risk due tothe presence of one or more risk factors (such as family history orexposure to infectious agent).

Isolated: An “isolated” biological component (such as a nucleic acid orprotein or organelle) has been substantially separated or purified awayfrom other biological components in the cell of the organism in whichthe component naturally occurs, i.e., other chromosomal andextra-chromosomal DNA and RNA, proteins and organelles. Nucleic acidsand proteins that have been “isolated” include nucleic acids andproteins purified by standard purification methods. The term alsoembraces nucleic acids and proteins prepared by recombinant expressionin a host cell as well as chemically synthesized nucleic acids.

A “purified antibody” is at least 60%, by weight free from proteins andnaturally occurring organic molecules with which it is naturallyassociated. In some examples the preparation is at least about 75%, atleast about 80%, at least about 90%, at least about 95%, or at leastabout 99%, by weight of antibody, such as a PD-1, PD-L1, or PD-L2specific antibody. A purified antibody can be obtained, for example, byaffinity chromatography using recombinantly-produced protein orconserved motif peptides and standard techniques.

Label: A detectable compound or composition that is conjugated directlyor indirectly to another molecule, such as an antibody or a protein, tofacilitate detection of that molecule. Specific, non-limiting examplesof labels include fluorescent tags, enzymatic linkages, and radioactiveisotopes. In one example, a “labeled antibody” refers to incorporationof another molecule in the antibody. For example, the label is adetectable marker, such as the incorporation of a radiolabeled aminoacid or attachment to a polypeptide of biotinyl moieties that can bedetected by marked avidin (for example, streptavidin containing afluorescent marker or enzymatic activity that can be detected by opticalor colorimetric methods). Various methods of labeling polypeptides andglycoproteins are known in the art and may be used. Examples of labelsfor polypeptides include, but are not limited to, the following:radioisotopes or radionucleotides (such as ³⁵S or ¹³¹I), fluorescentlabels (such as fluorescein isothiocyanate (FITC), rhodamine, lanthanidephosphors), enzymatic labels (such as horseradish peroxidase,beta-galactosidase, luciferase, alkaline phosphatase), chemiluminescentmarkers, biotinyl groups, predetermined polypeptide epitopes recognizedby a secondary reporter (such as a leucine zipper pair sequences,binding sites for secondary antibodies, metal binding domains, epitopetags), or magnetic agents, such as gadolinium chelates. In someembodiments, labels are attached by spacer arms of various lengths toreduce potential steric hindrance.

Lymphocytes: A type of white blood cell that is involved in the immunedefenses of the body. There are two main types of lymphocytes: B cellsand T cells.

Major Histocompatibility Complex (MHC): A generic designation meant toencompass the histocompatibility antigen systems described in differentspecies, including the human leukocyte antigens (“HLA”).

Mammal: This term includes both human and non-human mammals. Similarly,the term “subject” includes both human and veterinary subjects.

Mean Fluorescence Intensity (flow cytometry): Flow cytometry isconcerned with the measurement of the light intensity of a cell orparticle, whether it be scattered laser light or fluorescence emitted bya fluorochrome. Light is detected by a photomultiplier tube (PMT) whichconverts it via an amplifier to a voltage that is proportional to theoriginal fluorescence intensity and the voltage on the PMT. Thesevoltages, which are a continuous distribution, are converted to adiscrete distribution by an Analog to Digital converter (ADC) whichplaces each signal into a specific channel depending on the level offluorescence. The greater the resolution of the ADC, the closer thisreflects the continuous distribution.

Flow cytometric data can be displayed using either a linear or alogarithmic scale. The use of a logarithmic scale is indicated in mostbiological situations where distributions are skewed to the right. Inthis case the effect is to normalize the distribution—it is said to beLog Normal and the data has been log-transformed. Linear signals comethrough a linear amplifier but the logarithmic transformation may beachieved either by a logarithmic amplifier or by the use of Look UpTables (LUT). Most ADCs in analytical cytometers are 10-bit, i.e., theydivide data into 2e10 or 1024 channels, although there is a growingtrend to use 12- or 14-bit ADCs to give greater resolution of data.

Data from a single data channel (scatter or fluorescence) is displayedas a histogram in which the x axis is divided into 1024 channels (for a10-bit ADC). If the data is in a linear scale, the channel number andthe linear value for that channel will be easily obtained. On alogarithmic scale, the x axis is still divided into 1024 channels but isdisplayed as a 4-log decade scale (in general 4 log decades are used).

To quantify flow cytometric data the measures of the distribution of apopulation are utilized. Generally, the measures of central tendency arethe mean and the median. The mean is the ‘average’ and can be eitherarithmetic or geometric. The arithmetic mean is calculated asSigma(x)/n, and the geometric mean as n root(a1×a2×a3 . . . an). Ingeneral, with log-amplified data the geometric mean is used as it takesinto account the weighting of the data distribution, and the arithmeticmean is used for linear data or data displayed on a linear scale. Themedian is the central value, i.e., the 50th percentile, where half thevalues are above and half below. A cell with “high” expression and “low”expression can be determined relatively depending on the fluorescence ofthe entire population; these parameters are readily visualized on plotsof flow cytometric data.

Neoplasm: An abnormal cellular proliferation, which includes benign andmalignant tumors, as well as other proliferative disorders.

Neutralizing antibody: An antibody which reduces the infectious titer ofan infectious agent by binding to a specific antigen on the infectiousagent. In some examples the infectious agent is a virus, bacteria orfungus.

Oligonucleotide: A linear polynucleotide sequence of up to about 100nucleotide bases in length.

Open reading frame (ORF): A series of nucleotide triplets (codons)coding for amino acids without any internal termination codons. Thesesequences are usually translatable into a peptide.

Operably linked: A first nucleic acid sequence is operably linked with asecond nucleic acid sequence when the first nucleic acid sequence isplaced in a functional relationship with the second nucleic acidsequence. For instance, a promoter is operably linked to a codingsequence if the promoter affects the transcription or expression of thecoding sequence. Generally, operably linked DNA sequences are contiguousand, where necessary to join two protein-coding regions, in the samereading frame.

Pharmaceutically acceptable carriers: The pharmaceutically acceptablecarriers of use are conventional. Remington's Pharmaceutical Sciences,by E. W. Martin, Mack Publishing Co., Easton, Pa., 15th Edition (1975),describes compositions and formulations suitable for pharmaceuticaldelivery of the fusion proteins herein disclosed.

In general, the nature of the carrier will depend on the particular modeof administration being employed. For instance, parenteral formulationsusually comprise injectable fluids that include pharmaceutically andphysiologically acceptable fluids such as water, physiological saline,balanced salt solutions, aqueous dextrose, glycerol or the like as avehicle. For solid compositions (such as powder, pill, tablet, orcapsule forms), conventional non-toxic solid carriers can include, forexample, pharmaceutical grades of mannitol, lactose, starch, ormagnesium stearate. In addition to biologically neutral carriers,pharmaceutical compositions to be administered can contain minor amountsof non-toxic auxiliary substances, such as wetting or emulsifyingagents, preservatives, and pH buffering agents and the like, for examplesodium acetate or sorbitan monolaurate.

A “therapeutically effective amount” is a quantity of a composition or acell to achieve a desired biological effect in a subject being treated.For instance, this can be the amount of a PD-1 antagonist necessary toinduce an immune response, inhibit tumor growth, induce memory B cellproliferation, or to measurably alter outward symptoms of a tumor orpersistent infection. When administered to a subject, a dosage willgenerally be used that will achieve target tissue concentrations (forexample, in lymphocytes) that has been shown to achieve an in vitroeffect.

In particular examples, a therapeutically effective amount is an amountof an agent, such as PD-1 antagonist, effective to induce theproliferation of memory B cells. In another particular example, atherapeutically effective amount is an amount of a PD-1 antagonist thatalters a sign or a symptom of a disorder in a subject, such as adisorder that can be improved by increasing a memory B cell responseand/or a T cell response.

An effective amount of an agent such as a PD-1 antagonist can beadministered in a single dose, or in several doses, for example daily,during a course of treatment. However, the effective amount of a PD-1antagonist will be dependent on the subject being treated, the severityand type of the condition being treated, and the manner ofadministration. The methods disclosed herein have equal application inmedical and veterinary settings. Therefore, the general term “subjectbeing treated” is understood to include all organisms (e.g., humans,apes, dogs, cats, horses, and cows) that require an increase in thedesired biological effect, such as an enhanced immune response.

Polynucleotide: The term polynucleotide or nucleic acid sequence refersto a polymeric form of nucleotide at least 10 bases in length. Arecombinant polynucleotide includes a polynucleotide that is notimmediately contiguous with both of the coding sequences with which itis immediately contiguous (one on the 5′ end and one on the 3′ end) inthe naturally occurring genome of the organism from which it is derived.The term therefore includes, for example, a recombinant DNA which isincorporated into a vector; into an autonomously replicating plasmid orvirus; or into the genomic DNA of a prokaryote or eukaryote, or whichexists as a separate molecule (e.g., a cDNA) independent of othersequences. The nucleotides can be ribonucleotides, deoxyribonucleotides,or modified forms of either nucleotide. The term includes single- anddouble-stranded forms of DNA.

Polypeptide: Any chain of amino acids, regardless of length orpost-translational modification (e.g., glycosylation orphosphorylation). A polypeptide can be between 3 and 30 amino acids inlength. In one embodiment, a polypeptide is from about 7 to about 25amino acids in length. In yet another embodiment, a polypeptide is fromabout 8 to about 10 amino acids in length. In yet another embodiment, apeptide is about 9 amino acids in length. With regard to polypeptides,“comprises” indicates that additional amino acid sequence or othermolecules can be included in the molecule, “consists essentially of”indicates that additional amino acid sequences are not included in themolecule, but that other agents (such as labels or chemical compounds)can be included, and “consists of” indicates that additional amino acidsequences and additional agents are not included in the molecule.

Proliferation: The division of a cell to produce progeny, which can bemeasured in a number of ways known in the art. This includes, but is notlimited to, assays that count the total number of cells, assays thatcount the number of cells of a specific cell type, KI-67 assays,thymidine incorporation, and bromodeoxyuridine assays.

Programmed Death (PD)-1: A protein that forms a complex with PD-L1 orPD-L2 protein and is involved in an immune response, such as theco-stimulation of T cells. Generally, PD-1 protein are substantiallyidentical to the naturally occurring (wild type) PD-1 (see, for example,Ishida et al. EMBO J. 11:3887-3895, 1992, Shinohara et al. Genomics23:704-706, 1994; and U.S. Pat. No. 5,698,520, all incorporated byreference herein in their entirety). In several examples, PD-1 signalingreduces, for example, CD8+ T cell cytoxicity by reducing T cellproliferation, cytokine production, or viral clearance. Thus, a PD-1polypeptide can reduce CD8+ T cell cytotoxic activity by at least 5%,10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more than 100% belowcontrol levels as measured by any standard method.

As used herein, the term “activity” with respect to a PD-1 polypeptideor protein includes any activity which is inherent to the naturallyoccurring PD-1 protein, such as the ability to modulate an inhibitorysignal in an activated immune cell, such as by engaging a natural ligandon an antigen presenting cell. Such modulation of an inhibitory signalin an immune cell results in modulation of proliferation and/or survivalof an immune cell and/or cytokine secretion by an immune cell. PD-1protein can also modulate a costimulatory signal by competing with acostimulatory receptor for binding of a B7 molecule. Thus, the term“PD-1 activity” includes the ability of a PD-1 polypeptide or protein tobind its natural ligand(s), the ability to modulate immune cellcostimulatory or inhibitory signals, and the ability to modulate theimmune response.

“Reduce the expression or activity of PD-1” refers to a decrease in thelevel or biological activity of PD-1 relative to the level or biologicalactivity of PD-1 protein in a control, such as an untreated subject orsample. In specific examples, the level or activity is reduced by atleast 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or even greaterthan 100%, relative to an untreated control. For example, the biologicalactivity of PD-1 protein is reduced if binding of PD-1 protein to PD-L1,PD-L2, or both is reduced, thereby resulting in a reduction in PD-1signaling and therefore resulting in an increase in CD8+ T cellcytotoxicity.

A “PD-1 gene” is a nucleic acid that encodes a PD-1 protein. A “PD-1fusion gene” is a PD-1 coding region operably linked to a second,heterologous nucleic acid sequence. A PD-1 fusion gene can include aPD-1 promoter, or can include a heterologous promoter. In someembodiments, the second, heterologous nucleic acid sequence is areporter gene, that is, a gene whose expression may be assayed; reportergenes include, without limitation, those encoding glucuronidase (GUS),luciferase, chloramphenicol transacetylase (CAT), green fluorescentprotein (GFP), alkaline phosphatase, and .beta.-galactosidase.

Sample (Biological sample): Includes biological samples containingfluids, tissues, cells, and subcomponents thereof, such as DNA, RNA, andproteins. For example, common samples in the context of the presentinvention include bone marrow, spleen, lymph node, blood, e.g.,peripheral blood (but can also include any other source from which Bcells or B cell progenitors can be isolated, including: urine, saliva,tissue biopsy, surgical specimens, fine needle aspirates, autopsymaterial, and the like).

Specific binding agent: An agent that binds substantially only to adefined target. Thus a PD-1 specific binding agent is an agent thatbinds substantially to a PD-1 polypeptide and not unrelatedpolypeptides. In one embodiment, the specific binding agent is amonoclonal or polyclonal antibody that specifically binds the PD-1,PD-L1 OR PD-L2 polypeptide.

The term “specifically binds” refers, with respect to an antigen such asPD-1, to the preferential association of an antibody or other ligand, inwhole or part, with a cell or tissue bearing that antigen and not tocells or tissues lacking that antigen. It is, of course, recognized thata certain degree of non-specific interaction may occur between amolecule and a non-target cell or tissue. Nevertheless, specific bindingmay be distinguished as mediated through specific recognition of theantigen. Although selectively reactive antibodies bind antigen, they maydo so with low affinity. Specific binding results in a much strongerassociation between the antibody (or other ligand) and cells bearing theantigen than between the antibody (or other ligand) and cells lackingthe antigen. Specific binding typically results in greater than 2-fold,such as greater than 5-fold, greater than 10-fold, or greater than100-fold increase in amount of bound antibody or other ligand (per unittime) to a cell or tissue bearing the PD-1 polypeptide as compared to acell or tissue lacking the polypeptide. Specific binding to a proteinunder such conditions requires an antibody that is selected for itsspecificity for a particular protein. A variety of immunoassay formatsare appropriate for selecting antibodies or other ligands specificallyimmunoreactive with a particular protein. For example, solid-phase ELISAimmunoassays are routinely used to select monoclonal antibodiesspecifically immunoreactive with a protein. See Harlow & Lane,Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, NewYork (1988), for a description of immunoassay formats and conditionsthat can be used to determine specific immunoreactivity.

T Cell: A white blood cell critical to the immune response. T cellsinclude, but are not limited to, CD4⁺ T cells and CD8+ T cells. A CD4⁺ Tlymphocyte is an immune cell that carries a marker on its surface knownas “cluster of differentiation 4” (CD4). These cells, also known ashelper T cells, help orchestrate the immune response, including antibodyresponses as well as killer T cell responses. CD8+ T cells carry the“cluster of differentiation 8” (CD8) marker. In one embodiment, a CD8+ Tcell is a cytotoxic T lymphocyte. In another embodiment, a CD8+ cell isa suppressor T cell. A T cell is “activated “when it can respond to aspecific antigen of interest presented on an antigen presenting cells.

Transduced/Transfected: A transduced cell is a cell into which has beenintroduced a nucleic acid molecule by molecular biology techniques. Asused herein, the term transduction encompasses all techniques by which anucleic acid molecule might be introduced into such a cell, includingtransfection with viral vectors, transformation with plasmid vectors,and introduction of naked DNA by electroporation, lipofection, andparticle gun acceleration.

Vector: A nucleic acid molecule as introduced into a host cell, therebyproducing a transformed host cell. A vector may include nucleic acidsequences that permit it to replicate in a host cell, such as an originof replication. A vector may also include one or more nucleic acidsencoding a selectable marker and other genetic elements known in theart. Vectors include plasmid vectors, including plasmids for expressionin gram negative and gram positive bacterial cells. Exemplary vectorsinclude those for expression in E. coli and Salmonella. Vectors alsoinclude viral vectors, such as, but are not limited to, retrovirus,orthopox, avipox, fowlpox, capripox, suipox, adenoviral, herpes virus,alpha virus, baculovirus, Sindbis virus, vaccinia virus and poliovirusvectors.

Unless otherwise explained, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this disclosure belongs. The singular terms“a,” “an,” and “the” include plural referents unless context clearlyindicates otherwise. Similarly, the word “or” is intended to include“and” unless the context clearly indicates otherwise. It is further tobe understood that all base sizes or amino acid sizes, and all molecularweight or molecular mass values, given for nucleic acids or polypeptidesare approximate, and are provided for description. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of this disclosure, suitable methods andmaterials are described below. The term “comprises” means “includes.”All publications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including explanations ofterms, will control. In addition, the materials, methods, and examplesare illustrative only and not intended to be limiting.

RELATED APPLICATIONS

The disclosed subject matter is also related to the subject matter ofPCT Application No. PCT/US2007/088851, filed Dec. 26, 2007, U.S.Provisional Application No. 60/688,872, filed Jun. 8, 2005, U.S. Utilityapplication Ser. No. 11/449,919, filed Jun. 8, 2006, and PCT ApplicationNo. PCT/US2006/22423, Jun. 8, 2006. This application is also related toU.S. Provisional Application No. 60/877,518, filed Dec. 27, 2006. Theseprior applications are incorporated herein by reference in theirentirety.

PD-1 Antagonists

The methods disclosed herein involve the use of inhibitors of the PD-1pathway (PD-1 antagonists). PD-1 molecules are members of theimmunoglobulin gene superfamily. The human PD-1 has an extracellularregion containing an immunoglobulin superfamily domain, a transmembranedomain, and an intracellular region including an immunoreceptortyrosine-based inhibitory motif (ITIM) ((Ishida et al., EMBO J. 11:3887,1992; Shinohara et al., Genomics 23:704, 1994; U.S. Pat. No. 5,698,520).These features also define a larger family of molecules, called theimmunoinhibitory receptors, which also includes gp49B, PIR-B, and thekiller inhibitory receptors (KIRs) (Vivier and Daeron (1997) Immunol.Today 18:286). Without being bound by theory, it is believed that thetyrosyl phosphorylated ITIM motif of these receptors interacts with theS112-domain containing phosphatase, which leads to inhibitory signals. Asubset of these immuno-inhibitory receptors bind to majorhistocompatibility complex (MHC) molecules, such as the KIRs, and CTLA4binds to B7-1 and B7-2.

In humans, PD-1 is a 50-55 kDa type I transmembrane receptor that wasoriginally identified in a T cell line undergoing activation-inducedapoptosis. PD-1 is expressed on T cells, B cells, and macrophages. Theligands for PD-1 are the B7 family members PD-ligand 1 (PD-L1, alsoknown as B7-H1) and PD-L2 (also known as B7-DC).

In vivo, PD-1 is expressed on activated T cells, B cells, and monocytes.Experimental data implicates the interactions of PD-1 with its ligandsin downregulation of central and peripheral immune responses. Inparticular, proliferation in wild-type T cells but not in PD-1-deficientT cells is inhibited in the presence of PD-L1. Additionally,PD-1-deficient mice exhibit an autoimmune phenotype.

An exemplary amino acid sequence of human PD-1 is set forth below (seealso Ishida et al., EMBO J. 11:3887, 1992; Shinohara et al. Genomics23:704, 1994; U.S. Pat. No. 5,698,520):

(SEQ ID NO: 1) mqipqapwpv vwavlqlgwr pgwfldspdr pwnpptffpallvvtegdna tftcsfsnts esfvlnwyrm spsnqtdklaafpedrsqpg qdcrfrvtql pngrdfhmsv vrarrndsgtylcgaislap kaqikeslra elrvterrae vptahpspsprpagqfqtlv vgvvggllgs lvllvwvlav icsraargtigarrtgqplk edpsavpvfs vdygeldfqw rektpeppvpcvpeqteyat ivfpsgmgts sparrgsadg prsaqplrpe dghcswpl An exemplary amino acid sequence of mouse PD-1 is set forth below:

(SEQ ID NO: 2) mwvrqvpwsf twavlqlswq sgwllevpng pwrsltfypawltvsegana tftcslsnws edlmlnwnrl spsnqtekqaafcnglsqpv qdarfqiiql pnrhdfhmni ldtrrndsgiylcgaislhp kakieespga elvvterile tstrypspspkpegrfqgmv igimsalvgi pvllllawal avfcstsmseargagskddt lkeepsaapv psvayeeldf qgrektpelptacvhteyat ivfteglgas amgrrgsadg lqgprpprhe dghcswpl

Additional amino acid sequences are disclosed in U.S. Pat. No. 6,808,710and U.S. Patent Application Publication Nos. 2004/0137577, 2003/0232323,2003/0166531, 2003/0064380, 2003/0044768, 2003/0039653, 2002/0164600,2002/0160000, 2002/0110836, 2002/0107363, and 2002/0106730, which areincorporated herein by reference. PD-1 is a member of the immunoglobulin(Ig) superfamily that contains a single Ig V-like domain in itsextracellular region. The PD-1 cytoplasmic domain contains twotyrosines, with the most membrane-proximal tyrosine (VAYEEL (see aminoacids 223-228 of SEQ ID NO: 2) in mouse PD-1) located within an ITIM(immuno-receptor tyrosine-based inhibitory motif). The presence of anITIM on PD-1 indicates that this molecule functions to attenuate antigenreceptor signaling by recruitment of cytoplasmic phosphatases. Human andmurine PD-1 proteins share about 60% amino acid identity withconservation of four potential N-glycosylation sites, and residues thatdefine the Ig-V domain. The ITIM in the cytoplasmic region and theITIM-like motif surrounding the carboxy-terminal tyrosine (TEYATI (seeamino acids 166-181 of SEQ ID NO: 2) in human and mouse, respectively)are also conserved between human and murine orthologues.

PD-1 is a member of the CD28/CTLA-4 family of molecules based on itsability to bind to PD-L1. In vivo, like CTLA4, PD-1 is rapidly inducedon the surface of T-cells in response to anti-CD3 (Agata et al. Int.Immunol. 8:765, 1996). In contrast to CTLA4, however, PD-1 is alsoinduced on the surface of B-cells (in response to anti-IgM). PD-1 isalso expressed on a subset of thymocytes and myeloid cells (Agata et al.(1996) supra; Nishimura et al. (1996) Int. Immunol. 8:773).

T cell anergy is concomitant with an induction in PD-1 expression. It isdisclosed herein that T-cell cytoxicity can be increased by contacting aT-cell with an agent that reduces the expression or activity of PD-1.More specifically, it is disclosed herein that an agent that reduces theexpression or activity of PD-1 can be used to increase an immuneresponse, such as to a viral antigen or a tumor antigen.

Without being bound by theory, reduction of PD-1 expression or activityresults in an increase in cytotoxic T cell activity, increasing thespecific immune response to the infectious agent. In order for T cellsto respond to foreign proteins, two signals must be provided byantigen-presenting cells (APCs) to resting T lymphocytes. The firstsignal, which confers specificity to the immune response, is transducedvia the T cell receptor (TCR) following recognition of foreign antigenicpeptide presented in the context of the major histocompatibility complex(MHC). The second signal, termed costimulation, induces T cells toproliferate and become functional. Costimulation is neitherantigen-specific, nor MHC-restricted and is provided by one or moredistinct cell surface polypeptides expressed by APCs. If T cells areonly stimulated through the T cell receptor, without receiving anadditional costimulatory signal, they become nonresponsive, anergic, ordie, resulting in downmodulation of the immune response.

The CD80 (B7-1) and CD86 (B7-2) proteins, expressed on APCs, arecritical costimulatory polypeptides. While B7-2 plays a predominant roleduring primary immune responses, B7-1 is upregulated later in the courseof an immune response to prolong primary T cell responses orcostimulating secondary T cell responses. B7 polypeptides are capable ofproviding costimulatory or inhibitory signals to immune cells to promoteor inhibit immune cell responses. For example, when bound to acostimulatory receptor, PD-L1 (B7-4) induces costimulation of immunecells or inhibits immune cell costimulation when present in a solubleform. When bound to an inhibitory receptor, PD-L1 molecules can transmitan inhibitory signal to an immune cell. Exemplary B7 family membersinclude B7-1, B7-2, B7-3 (recognized by the antibody BB-1), B7h (PD-L1),and B7-4 and soluble fragments or derivatives thereof. B7 family membersbind to one or more receptors on an immune cell, such as CTLA4, CD28,ICOS, PD-1 and/or other receptors, and, depending on the receptor, havethe ability to transmit an inhibitory signal or a costimulatory signalto an immune cell.

CD28 is a receptor that is constitutively expressed on resting T cells.After signaling through the T cell receptor, ligation of CD28 andtransduction of a costimulatory signal induces T cells to proliferateand secrete IL-2. CTLA4 (CD152), a receptor homologous to CD28, isabsent on resting T cells but its expression is induced following T cellactivation. CTLA4 plays a role in negative regulation of T cellresponses. ICOS, a polypeptide related to CD28 and CTLA4, is involved inIL-10 production. PD-1, the receptor to which PD-L1 and PD-L2 bind, isalso rapidly induced on the surface of T-cells. PD-1 is also expressedon the surface of B-cells (in response to anti-IgM) and on a subset ofthymocytes and myeloid cells.

Engagement of PD-1 (for example by crosslinking or by aggregation),leads to the transmission of an inhibitory signal in an immune cell,resulting in a reduction of immune responses concomitant with anincrease in immune cell anergy. PD-1 family members bind to one or morereceptors, such as PD-L1 and PD-L2 on antigen presenting cells. PD-L1and PD-L2, both of which are human PD-1 ligand polypeptides, are membersof the B7 family of polypeptides (see above). Each PD-1 ligand containsa signal sequence, an IgV domain, an IgC domain, a transmembrane domain,and a short cytoplasmic tail. In vivo, these ligands have been shown tobe expressed in placenta, spleen, lymph nodes, thymus, and heart. PD-L2is also expressed in the pancreas, lung, and liver, while PD-L1 isexpressed in fetal liver, activated T-cells and endothelial cells.Expression of both PD-1 ligands are upregulated on activated monocytesand dendritic cells.

An exemplary amino acid sequence for PD-L1 (GENBANK® Accession No.AAG18508, as available Oct. 4, 2000) is set forth below:

(SEQ ID NO: 3) mrifavfifm tywhllnaft vtvpkdlyvv eygsnmtieckfpvekqldl aalivyweme dkniiqfvhg eedlkvqhssyrqrarllkd qlslgnaalq itdvklqdag vyrcmisyggadykritvkv napynkinqr ilvvdpvtse heltcqaegypkaeviwtss dhqvlsgktt ttnskreekl fnvtstlrintttneifyct frrldpeenh taelvipelp lahppnerthlvilgaillc lgvaltfifr lrkgrmmdvk kcgiqdtnsk kqsdthleet 

An exemplary PD-L2 precursor amino acid sequence (GENBANK® Accession No.AAK15370, as available Apr. 8, 2002) is set forth below:

(SEQ ID NO: 4) miflllmlsl elqlhqiaal ftvtvpkely iiehgsnvtlecnfdtgshv nlgaitaslq kvendtsphr eratlleeqlplgkasfhip qvqvrdegqy qciiiygvaw dykyltlkvkasyrkinthi lkvpetdeve ltcqatgypl aevswpnvsvpantshsrtp eglyqvtsvl rlkpppgrnf scvfwnthvreltlasidlq sqmeprthpt wllhifipsc iiafifiatvialrkqlcqk lysskdttkr pvtttkrevn sai

An exemplary variant PD-L2 precursor amino acid sequence (GENBANK®Accession No. Q9BQ51, as available Dec. 12, 2006) is set forth below:

(SEQ ID NO: 46) miflllmlsl elqlhqiaal ftvtvpkely iiehgsnvtlecnfdtgshv nlgaitaslq kvendtsphr eratlleeqlplgkasfhip qvqvrdegqy qciiiygvaw dykyltlkvkasyrkinthi lkvpetdeve ltcqatgypl aevswpnvsvpantshsrtp eglyqvtsvl rlkpppgrnf scvfwnthvreltlasidlq sqmeprthpt wllhifipfc iiafifiatvialrkqlcqk lysskdttkr pvtttkrevn sai

PD-1 antagonists include agents that reduce the expression or activityof a PD ligand 1 (PD-L1) or a PD ligand 2 (PD-L2) or reduces theinteraction between PD-1 and PD-L1 or the interaction between PD-1 andPD-L2. Exemplary compounds include antibodies (such as an anti-PD-1antibody, an anti-PD-L1 antibody, and an anti-PD-L2 antibody), RNAimolecules (such as anti-PD-1 RNAi molecules, anti-PD-L1 RNAi, and ananti-PD-L2 RNAi), antisense molecules (such as an anti-PD-1 antisenseRNA, an anti-PD-L1 antisense RNA, and an anti-PD-L2 antisense RNA),dominant negative proteins (such as a dominant negative PD-1 protein, adominant negative PD-L1 protein, and a dominant negative PD-L2 protein),and small molecule inhibitors.

An antagonist of PD-1 is any agent having the ability to reduce theexpression or the activity of PD-1 in a cell. PD-1 expression oractivity is reduced by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90%, or 100% compared to such expression or activity in a control.Exemplary reductions in activity are at least about 50%, at least about60%, at least about 70%, at least about 80%, at least about 90%, atleast about 95%, or a complete absence of detectable activity. In oneexample, the control is a cell that has not been treated with the PD-1antagonist. In another example, the control is a standard value, or acell contacted with an agent, such as a carrier, known not to affectPD-1 activity. PD-1 expression or activity can be determined by anystandard method in the art, including those described herein.Optionally, the PD-1 antagonist inhibits or reduces binding of PD-1 toPD-L1, PD-L2, or both.

A. Antibodies

Antibodies that specifically bind PD-1, PD-L1 or PD-L2 (or a combinationthereof) are of use in the methods disclosed herein. Antibodies includemonoclonal antibodies, humanized antibodies, deimmunized antibodies, andimmunoglobulin (Ig) fusion proteins. Polyclonal anti-PD-1, anti-PDL1 orPD-L2 antibodies can be prepared by one of skill in the art, such as byimmunizing a suitable subject (such as a veterinary subject) with a PD-1ligand or PD-1 immunogen. The anti-PD-1, anti-PD-L1 or anti-PD-L2antibody titer in the immunized subject can be monitored over time bystandard techniques, such as with an enzyme linked immunosorbent assay(ELISA) using immobilized a PD-1 ligand or PD-1 polypeptide.

In one example, the antibody molecules that specifically bind PD-1,PD-L1 or PD-L2 (or combinations thereof) can be isolated from the mammal(such as from serum) and further purified by techniques known to one ofskill in the art. For example, antibodies can be purified using proteinA chromatography to isolate IgG antibodies.

Antibody-producing cells can be obtained from the subject and used toprepare monoclonal antibodies by standard techniques (see Kohler andMilstein Nature 256:495 49, 1995; Brown et al., J. Immunol. 127:539 46,1981; Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R.Liss, Inc., pp. 77 96, 1985; Gefter, M. L. et al. (1977) Somatic CellGenet. 3:231 36; Kenneth, R. H. in Monoclonal Antibodies: A NewDimension In Biological Analyses. Plenum Publishing Corp., New York,N.Y. (1980); Kozbor et al. Immunol. Today 4:72, 1983; Lerner, E. A.(1981) Yale J. Biol. Med. 54:387 402; Yeh et al., Proc. Natl. Acad. Sci.76:2927 31, 1976). In one example, an immortal cell line (typically amyeloma) is fused to lymphocytes (typically splenocytes) from a mammalimmunized with PD-1, PD-L1 or PD-L2, and the culture supernatants of theresulting hybridoma cells are screened to identify a hybridoma producinga monoclonal antibody that specifically binds to the polypeptide ofinterest.

In one embodiment, to produce a hybridoma, an immortal cell line (suchas a myeloma cell line) is derived from the same mammalian species asthe lymphocytes. For example, murine hybridomas can be made by fusinglymphocytes from a mouse immunized with a PD-1, PD-L1 or PD-L2 peptidewith an immortalized mouse cell line. In one example, a mouse myelomacell line is utilized that is sensitive to culture medium containinghypoxanthine, aminopterin and thymidine (“HAT medium”). Any of a numberof myeloma cell lines can be used as a fusion partner according tostandard techniques, including, for example, P3-NS1/1-Ag4-1,P3-x63-Ag8.653 or Sp2/O-Ag14 myeloma lines, which are available from theAmerican Type Culture Collection (ATCC), Rockville, Md. HAT-sensitivemouse myeloma cells can be fused to mouse splenocytes using polyethyleneglycol (“PEG”). Hybridoma cells resulting from the fusion are thenselected using HAT medium, which kills unfused (and unproductivelyfused) myeloma cells. Hybridoma cells producing a monoclonal antibody ofinterest can be detected, for example, by screening the hybridomaculture supernatants for the production antibodies that bind a PD-1,PD-L1 or PD-L2 molecule, such as by using an immunological assay (suchas an enzyme-linked immunosorbant assay(ELISA) or radioimmunoassay(RIA).

As an alternative to preparing monoclonal antibody-secreting hybridomas,a monoclonal antibody that specifically binds PD-1, PD-L1 or PD-L2 canbe identified and isolated by screening a recombinant combinatorialimmunoglobulin library (such as an antibody phage display library) withPD-1, PD-L1 or PD-L2 to isolate immunoglobulin library members thatspecifically bind the polypeptide. Kits for generating and screeningphage display libraries are commercially available (such as, but notlimited to, Pharmacia and Stratagene). Examples of methods and reagentsparticularly amenable for use in generating and screening antibodydisplay library can be found in, for example, U.S. Pat. No. 5,223,409;PCT Publication No. WO 90/02809; PCT Publication No. WO 91/17271; PCTPublication No. WO 92/18619; PCT Publication WO 92/20791; PCTPublication No. WO 92/15679; PCT Publication No. WO 92/01047; PCTPublication WO 93/01288; PCT Publication No. WO 92/09690; Barbas et al.,Proc. Natl. Acad. Sci. USA 88:7978 7982, 1991; Hoogenboom et al.,Nucleic Acids Res. 19:4133 4137, 1991.

The amino acid sequence of antibodies that bind PD-1 are disclosed, forexample, in U.S. Patent Publication No. 2006/0210567, which isincorporated herein by reference. Antibodies that bind PD-1 are alsodisclosed in U.S. Patent Publication No. 2006/0034826, which is alsoincorporated herein by reference. In several examples, the antibodyspecifically binds PD-1 or a PD-1 or PD-2 ligand with an affinityconstant of at least 10⁷ M⁻¹, such as at least 10⁸ M⁻¹ at least 5×10⁸M⁻¹ or at least 10⁹ M⁻¹.

In one example the sequence of the specificity determining regions ofeach CDR is determined Residues are outside the SDR (non-ligandcontacting sites) are substituted. For example, in any of the CDRsequences, at most one, two or three amino acids can be substituted. Theproduction of chimeric antibodies, which include a framework region fromone antibody and the CDRs from a different antibody, is well known inthe art. For example, humanized antibodies can be routinely produced.The antibody or antibody fragment can be a humanized immunoglobulinhaving complementarity determining regions (CDRs) from a donormonoclonal antibody that binds PD-1, PD-L1 or PD-L2, and immunoglobulinand heavy and light chain variable region frameworks from human acceptorimmunoglobulin heavy and light chain frameworks. Generally, thehumanized immunoglobulin specifically binds to PD-1, PD-L1 or PD-L2 withan affinity constant of at least 10⁷ M⁻¹, such as at least 10⁸ M⁻¹ atleast 5×10⁸ M⁻¹ or at least 10⁹ M⁻¹.

Humanized monoclonal antibodies can be produced by transferring donorcomplementarity determining regions (CDRs) from heavy and light variablechains of the donor mouse immunoglobulin (such PD-1, PD-L1 or PD-L2)into a human variable domain, and then substituting human residues inthe framework regions when required to retain affinity. The use ofantibody components derived from humanized monoclonal antibodiesobviates potential problems associated with the immunogenicity of theconstant regions of the donor antibody. Techniques for producinghumanized monoclonal antibodies are described, for example, by Jones etal., Nature 321:522, 1986; Riechmann et al., Nature 332:323, 1988;Verhoeyen et al., Science 239:1534, 1988; Carter et al., Proc. Natl.Acad. Sci. U.S.A. 89:4285, 1992; Sandhu, Crit. Rev. Biotech. 12:437,1992; and Singer et al., J. Immunol. 150:2844, 1993. The antibody may beof any isotype, but in several embodiments the antibody is an IgG,including but not limited to, IgG₁, IgG₂, IgG₃ and IgG₄.

In one embodiment, the sequence of the humanized immunoglobulin heavychain variable region framework can be at least about 65% identical tothe sequence of the donor immunoglobulin heavy chain variable regionframework. Thus, the sequence of the humanized immunoglobulin heavychain variable region framework can be at least about 75%, at leastabout 85%, at least about 99% or at least about 95%, identical to thesequence of the donor immunoglobulin heavy chain variable regionframework. Human framework regions, and mutations that can be made inhumanized antibody framework regions, are known in the art (see, forexample, in U.S. Pat. No. 5,585,089, which is incorporated herein byreference).

Exemplary human antibodies are LEN and 21/28 CL. The sequences of theheavy and light chain frameworks are known in the art. Exemplary lightchain frameworks of human MAb LEN have the following sequences:

(SEQ ID NO: 5) FR1: DIVMTQS PDSLAVSLGERATINC  (SEQ ID NO: 6)FR2: WYQQKPGQPPLLIY  (SEQ ID NO: 7)FR3: GVPDRPFGSGSGTDFTLTISSLQAEDVAVYYC  (SEQ ID NO: 8) FR4: FGQGQTKLEIK

Exemplary heavy chain frameworks of human MAb 21/28′ CL have thefollowing sequences:

(SEQ ID NO: 9) FR1: QVQLVQSGAEVKKPQASVKVSCKASQYTFT  (SEQ ID NO: 10)FR2: WVRQAPGQRLEWMG  (SEQ ID NO: 11)FR3: RVTITRDTSASTAYMELSSLRSEDTAVYYCAR (SEQ ID NO: 12) FR4: WGQGTLVTVSS.

Antibodies, such as murine monoclonal antibodies, chimeric antibodies,and humanized antibodies, include full length molecules as well asfragments thereof, such as Fab, F(ab′)2, and Fv which include a heavychain and light chain variable region and are capable of bindingspecific epitope determinants. These antibody fragments retain someability to selectively bind with their antigen or receptor. Thesefragments include:

(1) Fab, the fragment which contains a monovalent antigen-bindingfragment of an antibody molecule, can be produced by digestion of wholeantibody with the enzyme papain to yield an intact light chain and aportion of one heavy chain;

(2) Fab′, the fragment of an antibody molecule can be obtained bytreating whole antibody with pepsin, followed by reduction, to yield anintact light chain and a portion of the heavy chain; two Fab′ fragmentsare obtained per antibody molecule;

(3) (Fab′)₂, the fragment of the antibody that can be obtained bytreating whole antibody with the enzyme pepsin without subsequentreduction; F(ab′)2 is a dimer of two Fab′ fragments held together by twodisulfide bonds;

(4) Fv, a genetically engineered fragment containing the variable regionof the light chain and the variable region of the heavy chain expressedas two chains; and

(5) Single chain antibody (such as scFv), defined as a geneticallyengineered molecule containing the variable region of the light chain,the variable region of the heavy chain, linked by a suitable polypeptidelinker as a genetically fused single chain molecule.

Methods of making these fragments are known in the art (see for example,Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring HarborLaboratory, New York, 1988). In several examples, the variable regionincludes the variable region of the light chain and the variable regionof the heavy chain expressed as individual polypeptides. Fv antibodiesare typically about 25 kDa and contain a complete antigen-binding sitewith three CDRs per each heavy chain and each light chain. To producethese antibodies, the V_(H) and the V_(L) can be expressed from twoindividual nucleic acid constructs in a host cell. If the V_(H) and theV_(L) are expressed non-contiguously, the chains of the Fv antibody aretypically held together by noncovalent interactions. However, thesechains tend to dissociate upon dilution, so methods have been developedto crosslink the chains through glutaraldehyde, intermoleculardisulfides, or a peptide linker. Thus, in one example, the Fv can be adisulfide stabilized Fv (dsFv), wherein the heavy chain variable regionand the light chain variable region are chemically linked by disulfidebonds.

In an additional example, the Fv fragments comprise V_(H) and V_(L)chains connected by a peptide linker. These single-chain antigen bindingproteins (scFv) are prepared by constructing a structural genecomprising DNA sequences encoding the V_(H) and V_(L) domains connectedby an oligonucleotide. The structural gene is inserted into anexpression vector, which is subsequently introduced into a host cellsuch as E. coli. The recombinant host cells synthesize a singlepolypeptide chain with a linker peptide bridging the two V domains.Methods for producing scFvs are known in the art (see Whitlow et al.,Methods: a Companion to Methods in Enzymology, Vol. 2, page 97, 1991;Bird et al., Science 242:423, 1988; U.S. Pat. No. 4,946,778; Pack etal., Bio/Technology 11:1271, 1993; and Sandhu, supra).

Antibody fragments can be prepared by proteolytic hydrolysis of theantibody or by expression in E. coli of DNA encoding the fragment.Antibody fragments can be obtained by pepsin or papain digestion ofwhole antibodies by conventional methods. For example, antibodyfragments can be produced by enzymatic cleavage of antibodies withpepsin to provide a 5S fragment denoted F(ab′)2. This fragment can befurther cleaved using a thiol reducing agent, and optionally a blockinggroup for the sulfhydryl groups resulting from cleavage of disulfidelinkages, to produce 3.5S Fab′ monovalent fragments. Alternatively, anenzymatic cleavage using pepsin produces two monovalent Fab′ fragmentsand an Fc fragment directly (see U.S. Pat. No. 4,036,945 and U.S. Pat.No. 4,331,647, and references contained therein; Nisonhoff et al., Arch.Biochem. Biophys. 89:230, 1960; Porter, Biochem. J. 73:119, 1959;Edelman et al., Methods in Enzymology, Vol. 1, page 422, Academic Press,1967; and Coligan et al. at sections 2.8.1-2.8.10 and 2.10.1-2.10.4).

Other methods of cleaving antibodies, such as separation of heavy chainsto form monovalent light-heavy chain fragments, further cleavage offragments, or other enzymatic, chemical, or genetic techniques may alsobe used, so long as the fragments bind to the antigen that is recognizedby the intact antibody.

One of skill will realize that conservative variants of the antibodiescan be produced. Such conservative variants employed in antibodyfragments, such as dsFv fragments or in scFv fragments, will retaincritical amino acid residues necessary for correct folding andstabilizing between the V_(H) and the V_(L) regions, and will retain thecharge characteristics of the residues in order to preserve the low pIand low toxicity of the molecules Amino acid substitutions (such as atmost one, at most two, at most three, at most four, or at most fiveamino acid substitutions) can be made in the V_(H) and the V_(L) regionsto increase yield. Conservative amino acid substitution tables providingfunctionally similar amino acids are well known to one of ordinary skillin the art. The following six groups are examples of amino acids thatare considered to be conservative substitutions for one another:

1) Alanine (A), Serine (S), Threonine (T);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

Thus, one of skill in the art can readily review the amino acid sequenceof an antibody of interest, locate one or more of the amino acids in thebrief table above, identify a conservative substitution, and produce theconservative variant using well-known molecular techniques.

Effector molecules, such as therapeutic, diagnostic, or detectionmoieties can be linked to an antibody that specifically binds PD-1,PD-L1 or PD-L2, using any number of means known to those of skill in theart. Both covalent and noncovalent attachment means may be used. Theprocedure for attaching an effector molecule to an antibody variesaccording to the chemical structure of the effector. Polypeptidestypically contain a variety of functional groups; such as carboxylicacid (COOH), free amine (—NH₂) or sulfhydryl (—SH) groups, which areavailable for reaction with a suitable functional group on an antibodyto result in the binding of the effector molecule. Alternatively, theantibody is derivatized to expose or attach additional reactivefunctional groups. The derivatization may involve attachment of any of anumber of linker molecules such as those available from Pierce ChemicalCompany, Rockford, Ill. The linker can be any molecule used to join theantibody to the effector molecule. The linker is capable of formingcovalent bonds to both the antibody and to the effector molecule.Suitable linkers are well known to those of skill in the art andinclude, but are not limited to, straight or branched-chain carbonlinkers, heterocyclic carbon linkers, or peptide linkers. Where theantibody and the effector molecule are polypeptides, the linkers may bejoined to the constituent amino acids through their side groups (such asthrough a disulfide linkage to cysteine) or to the alpha carbon aminoand carboxyl groups of the terminal amino acids.

Nucleic acid sequences encoding the antibodies can be prepared by anysuitable method including, for example, cloning of appropriate sequencesor by direct chemical synthesis by methods such as the phosphotriestermethod of Narang et al., Meth. Enzymol. 68:90-99, 1979; thephosphodiester method of Brown et al., Meth. Enzymol. 68:109-151, 1979;the diethylphosphoramidite method of Beaucage et al., Tetra. Lett.22:1859-1862, 1981; the solid phase phosphoramidite triester methoddescribed by Beaucage & Caruthers, Tetra. Letts. 22(20):1859-1862, 1981,for example, using an automated synthesizer as described in, forexample, Needham-VanDevanter et al., Nucl. Acids Res. 12:6159-6168,1984; and, the solid support method of U.S. Pat. No. 4,458,066. Chemicalsynthesis produces a single stranded oligonucleotide. This can beconverted into double stranded DNA by hybridization with a complementarysequence, or by polymerization with a DNA polymerase using the singlestrand as a template. One of skill would recognize that while chemicalsynthesis of DNA is generally limited to sequences of about 100 bases,longer sequences may be obtained by the ligation of shorter sequences.

Exemplary nucleic acids encoding sequences encoding an antibody thatspecifically binds PD-1, PD-L1 or PD-L2 can be prepared by cloningtechniques. Examples of appropriate cloning and sequencing techniques,and instructions sufficient to direct persons of skill through manycloning exercises are found in Sambrook et al., supra, Berger and Kimmel(eds.), supra, and Ausubel, supra. Product information frommanufacturers of biological reagents and experimental equipment alsoprovide useful information. Such manufacturers include the SIGMAChemical Company (Saint Louis, Mo.), R&D Systems (Minneapolis, Minn.),Pharmacia Amersham (Piscataway, N.J.), CLONTECH Laboratories, Inc. (PaloAlto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee,Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc.(Gaithersburg, Md.), Fluka Chemica-Biochemika Analytika (Fluka ChemieAG, Buchs, Switzerland), Invitrogen (San Diego, Calif.), and AppliedBiosystems (Foster City, Calif.), as well as many other commercialsources known to one of skill.

Nucleic acids can also be prepared by amplification methods.Amplification methods include polymerase chain reaction (PCR), theligase chain reaction (LCR), the transcription-based amplificationsystem (TAS), the self-sustained sequence replication system (3SR). Awide variety of cloning methods, host cells, and in vitro amplificationmethodologies are well known to persons of skill.

In one example, an antibody of use is prepared by inserting the cDNAwhich encodes a variable region from an antibody that specifically bindsPD-1, PD-L1 or PD-L2 into a vector which comprises the cDNA encoding aneffector molecule (EM). The insertion is made so that the variableregion and the EM are read in frame so that one continuous polypeptideis produced. Thus, the encoded polypeptide contains a functional Fvregion and a functional EM region. In one embodiment, cDNA encoding adetectable marker (such as an enzyme) is ligated to a scFv so that themarker is located at the carboxyl terminus of the scFv. In anotherexample, a detectable marker is located at the amino terminus of thescFv. In a further example, cDNA encoding a detectable marker is ligatedto a heavy chain variable region of an antibody that specifically bindsPD-1, PD-L1 or PD-L2, so that the marker is located at the carboxylterminus of the heavy chain variable region. The heavy chain-variableregion can subsequently be ligated to a light chain variable region ofthe antibody that specifically binds PD-1, PD-L1 or PD-L2 usingdisulfide bonds. In a yet another example, cDNA encoding a marker isligated to a light chain variable region of an antibody that binds PD-1,PD-L1 or PD-L2, so that the marker is located at the carboxyl terminusof the light chain variable region. The light chain-variable region cansubsequently be ligated to a heavy chain variable region of the antibodythat specifically binds PD-1, PD-L1 or PD-L2 using disulfide bonds.

Once the nucleic acids encoding the antibody or functional fragmentthereof are isolated and cloned, the protein can be expressed in arecombinantly engineered cell such as bacteria, plant, yeast, insect andmammalian cells. One or more DNA sequences encoding the antibody orfunctional fragment thereof can be expressed in vitro by DNA transferinto a suitable host cell. The cell may be prokaryotic or eukaryotic.The term also includes any progeny of the subject host cell. It isunderstood that all progeny may not be identical to the parental cellsince there may be mutations that occur during replication. Methods ofstable transfer, meaning that the foreign DNA is continuously maintainedin the host, are known in the art.

Polynucleotide sequences encoding the antibody or functional fragmentthereof can be operatively linked to expression control sequences. Anexpression control sequence operatively linked to a coding sequence isligated such that expression of the coding sequence is achieved underconditions compatible with the expression control sequences. Theexpression control sequences include, but are not limited to appropriatepromoters, enhancers, transcription terminators, a start codon (i.e.,ATG) in front of a protein-encoding gene, splicing signal for introns,maintenance of the correct reading frame of that gene to permit propertranslation of mRNA, and stop codons.

The polynucleotide sequences encoding the antibody or functionalfragment thereof can be inserted into an expression vector including,but not limited to a plasmid, virus or other vehicle that can bemanipulated to allow insertion or incorporation of sequences and can beexpressed in either prokaryotes or eukaryotes. Hosts can includemicrobial, yeast, insect and mammalian organisms. Methods of expressingDNA sequences having eukaryotic or viral sequences in prokaryotes arewell known in the art. Biologically functional viral and plasmid DNAvectors capable of expression and replication in a host are known in theart.

Transformation of a host cell with recombinant DNA may be carried out byconventional techniques as are well known to those skilled in the art.Where the host is prokaryotic, such as E. coli, competent cells whichare capable of DNA uptake can be prepared from cells harvested afterexponential growth phase and subsequently treated by the CaCl₂ methodusing procedures well known in the art. Alternatively, MgCl₂ or RbCl canbe used. Transformation can also be performed after forming a protoplastof the host cell if desired, or by electroporation.

When the host is a eukaryote, such methods of transfection of DNA ascalcium phosphate coprecipitates, conventional mechanical proceduressuch as microinjection, electroporation, insertion of a plasmid encasedin liposomes, or virus vectors may be used. Eukaryotic cells can also becotransformed with polynucleotide sequences encoding the antibody offunctional fragment thereof and a second foreign DNA molecule encoding aselectable phenotype, such as the herpes simplex thymidine kinase gene.Another method is to use a eukaryotic viral vector, such as simian virus40 (SV40) or bovine papilloma virus, to transiently infect or transformeukaryotic cells and express the protein (see for example, EukaryoticViral Vectors, Cold Spring Harbor Laboratory, Gluzman ed., 1982). One ofskill in the art can readily use expression systems such as plasmids andvectors of use in producing proteins in cells including highereukaryotic cells such as the COS, CHO, HeLa and myeloma cell lines.

Isolation and purification of recombinantly expressed polypeptide can becarried out by conventional means including preparative chromatographyand immunological separations. Once expressed, the recombinantantibodies can be purified according to standard procedures of the art,including ammonium sulfate precipitation, affinity columns, columnchromatography, and the like (see, generally, R. Scopes, ProteinPurification, Springer-Verlag, N.Y., 1982). Substantially purecompositions of at least about 90 to 95% homogeneity are disclosedherein, and 98 to 99% or more homogeneity can be used for pharmaceuticalpurposes. Once purified, partially or to homogeneity as desired, if tobe used therapeutically, the polypeptides should be substantially freeof endotoxin.

Methods for expression of single chain antibodies and/or refolding to anappropriate active form, including single chain antibodies, frombacteria such as E. coli have been described and are well-known and areapplicable to the antibodies disclosed herein. See, Buchner et al.,Anal. Biochem. 205:263-270, 1992; Pluckthun, Biotechnology 9:545, 1991;Huse et al., Science 246:1275, 1989 and Ward et al., Nature 341:544,1989, all incorporated by reference herein.

Often, functional heterologous proteins from E. coli or other bacteriaare isolated from inclusion bodies and require solubilization usingstrong denaturants, and subsequent refolding. During the solubilizationstep, as is well known in the art, a reducing agent must be present toseparate disulfide bonds. An exemplary buffer with a reducing agent is:0.1 M Tris pH 8, 6 M guanidine, 2 mM EDTA, 0.3 M DTE (dithioerythritol).Reoxidation of the disulfide bonds can occur in the presence of lowmolecular weight thiol reagents in reduced and oxidized form, asdescribed in Saxena et al., Biochemistry 9: 5015-5021, 1970,incorporated by reference herein, and especially as described by Buchneret al., supra.

Renaturation is typically accomplished by dilution (for example,100-fold) of the denatured and reduced protein into refolding buffer. Anexemplary buffer is 0.1 M Tris, pH 8.0, 0.5 M L-arginine, 8 mM oxidizedglutathione (GSSG), and 2 mM EDTA.

As a modification to the two chain antibody purification protocol, theheavy and light chain regions are separately solubilized and reduced andthen combined in the refolding solution. An exemplary yield is obtainedwhen these two proteins are mixed in a molar ratio such that a 5 foldmolar excess of one protein over the other is not exceeded. It isdesirable to add excess oxidized glutathione or other oxidizing lowmolecular weight compounds to the refolding solution after theredox-shuffling is completed.

In addition to recombinant methods, the antibodies and functionalfragments thereof that are disclosed herein can also be constructed inwhole or in part using standard peptide synthesis. Solid phase synthesisof the polypeptides of less than about 50 amino acids in length can beaccomplished by attaching the C-terminal amino acid of the sequence toan insoluble support followed by sequential addition of the remainingamino acids in the sequence. Techniques for solid phase synthesis aredescribed by Barany & Merrifield, The Peptides: Analysis, Synthesis,Biology. Vol. 2: Special Methods in Peptide Synthesis, Part A. pp.3-284; Merrifield et al., J. Am. Chem. Soc. 85:2149-2156, 1963, andStewart et al., Solid Phase Peptide Synthesis, 2nd ed., Pierce Chem.Co., Rockford, Ill., 1984. Proteins of greater length may be synthesizedby condensation of the amino and carboxyl termini of shorter fragments.Methods of forming peptide bonds by activation of a carboxyl terminalend (such as by the use of the coupling reagent N,N′-dicycylohexylcarbodimide) are well known in the art.

B. Inhibitory Nucleic Acids

Inhibitory nucleic acids that decrease the expression and/or activity ofPD-1, PD-L1 or PD-L2 can also be used in the methods disclosed herein.One embodiment is a small inhibitory RNA (siRNA) for interference orinhibition of expression of a target gene. Nucleic acid sequencesencoding PD-1, PD-L1 and PD-L2 are disclosed in GENBANK® Accession Nos.NM_(—)005018, AF344424, NP_(—)079515, and NP_(—)054862.

Generally, siRNAs are generated by the cleavage of relatively longdouble-stranded RNA molecules by Dicer or DCL enzymes (Zamore, Science,296:1265-1269, 2002; Bernstein et al., Nature, 409:363-366, 2001). Inanimals and plants, siRNAs are assembled into RISC and guide thesequence specific ribonucleolytic activity of RISC, thereby resulting inthe cleavage of mRNAs or other RNA target molecules in the cytoplasm. Inthe nucleus, siRNAs also guide heterochromatin-associated histone andDNA methylation, resulting in transcriptional silencing of individualgenes or large chromatin domains. PD-1 siRNAs are commerciallyavailable, such as from Santa Cruz Biotechnology, Inc.

The present disclosure provides RNA suitable for interference orinhibition of expression of a target gene, which RNA includes doublestranded RNA of about 15 to about 40 nucleotides containing a 0 to5-nucleotide 3′ and/or 5′ overhang on each strand. The sequence of theRNA is substantially identical to a portion of an mRNA or transcript ofa target gene, such as PD-1, PD-L1 or PD-L2) for which interference orinhibition of expression is desired. For purposes of this disclosure, asequence of the RNA “substantially identical” to a specific portion ofthe mRNA or transcript of the target gene for which interference orinhibition of expression is desired differs by no more than about 30percent, and in some embodiments no more than about 10 percent, from thespecific portion of the mRNA or transcript of the target gene. Inparticular embodiments, the sequence of the RNA is exactly identical toa specific portion of the mRNA or transcript of the target gene.

Thus, siRNAs disclosed herein include double-stranded RNA of about 15 toabout 40 nucleotides in length and a 3′ or 5′ overhang having a lengthof 0 to 5-nucleotides on each strand, wherein the sequence of the doublestranded RNA is substantially identical to (see above) a portion of amRNA or transcript of a nucleic acid encoding PD-1, PD-L1 or PD-L2. Inparticular examples, the double stranded RNA contains about 19 to about25 nucleotides, for instance 20, 21, or 22 nucleotides substantiallyidentical to a nucleic acid encoding PD-1, PD-L1 or PD-L2. In additionalexamples, the double stranded RNA contains about 19 to about 25nucleotides 100% identical to a nucleic acid encoding PD-1, PD-L1 orPD-L2. It should be not that in this context “about” refers to integeramounts only. In one example, “about” 20 nucleotides refers to anucleotide of 19 to 21 nucleotides in length.

Regarding the overhang on the double-stranded RNA, the length of theoverhang is independent between the two strands, in that the length ofone overhang is not dependent on the length of the overhang on otherstrand. In specific examples, the length of the 3′ or 5′ overhang is0-nucleotide on at least one strand, and in some cases it is0-nucleotide on both strands (thus, a blunt dsRNA). In other examples,the length of the 3′ or 5′ overhang is 1-nucleotide to 5-nucleotides onat least one strand. More particularly, in some examples the length ofthe 3′ or 5′ overhang is 2-nucleotides on at least one strand, or2-nucleotides on both strands. In particular examples, the dsRNAmolecule has 3′ overhangs of 2-nucleotides on both strands.

Thus, in one particular provided RNA embodiment, the double-stranded RNAcontains 20, 21, or 22 nucleotides, and the length of the 3′ overhang is2-nucleotides on both strands. In embodiments of the RNAs providedherein, the double-stranded RNA contains about 40-60% adenine+uracil(AU) and about 60-40% guanine+cytosine (GC). More particularly, inspecific examples the double-stranded RNA contains about 50% AU andabout 50% GC.

Also described herein are RNAs that further include at least onemodified ribonucleotide, for instance in the sense strand of thedouble-stranded RNA. In particular examples, the modified ribonucleotideis in the 3′ overhang of at least one strand, or more particularly inthe 3′ overhang of the sense strand. It is particularly contemplatedthat examples of modified ribonucleotides include ribonucleotides thatinclude a detectable label (for instance, a fluorophore, such asrhodamine or FITC), a thiophosphate nucleotide analog, a deoxynucleotide(considered modified because the base molecule is ribonucleic acid), a2′-fluorouracil, a 2′-aminouracil, a 2′-aminocytidine, a 4-thiouracil, a5-bromouracil, a 5-iodouracil, a 5-(3-aminoallyl)-uracil, an inosine, ora 2′O-Me-nucleotide analog.

Antisense and ribozyme molecules for PD-1, PD-L1 and PD-L2 are also ofuse in the method disclosed herein. Antisense nucleic acids are DNA orRNA molecules that are complementary to at least a portion of a specificmRNA molecule (Weintraub, Scientific American 262:40, 1990). In thecell, the antisense nucleic acids hybridize to the corresponding mRNA,forming a double-stranded molecule. The antisense nucleic acidsinterfere with the translation of the mRNA, since the cell will nottranslate an mRNA that is double-stranded. Antisense oligomers of about15 nucleotides are preferred, since they are easily synthesized and areless likely to cause problems than larger molecules when introduced intothe target cell producing PD-1, PD-L1 or PD-L2. The use of antisensemethods to inhibit the in vitro translation of genes is well known inthe art (see, for example, Marcus-Sakura, Anal. Biochem. 172:289, 1988).

An antisense oligonucleotide can be, for example, about 5, 10, 15, 20,25, 30, 35, 40, 45 or 50 nucleotides in length. An antisense nucleicacid can be constructed using chemical synthesis and enzymatic ligationreactions using procedures known in the art. For example, an antisensenucleic acid molecule can be chemically synthesized using naturallyoccurring nucleotides or variously modified nucleotides designed toincrease the biological stability of the molecules or to increase thephysical stability of the duplex formed between the antisense and sensenucleic acids, such as phosphorothioate derivatives and acridinesubstituted nucleotides can be used. Examples of modified nucleotideswhich can be used to generate the antisense nucleic acid include5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil,hypoxanthine, xantine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridin-e,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, amongst others.

Use of an oligonucleotide to stall transcription is known as the triplexstrategy since the bloomer winds around double-helical DNA, forming athree-strand helix. Therefore, these triplex compounds can be designedto recognize a unique site on a chosen gene (Maher, et al., AntisenseRes. and Dev. 1(3):227, 1991; Helene, C., Anticancer Drug Design6(6):569), 1991. This type of inhibitory oligonucleotide is also of usein the methods disclosed herein.

Ribozymes, which are RNA molecules possessing the ability tospecifically cleave other single-stranded RNA in a manner analogous toDNA restriction endonucleases, are also of use. Through the modificationof nucleotide sequences which encode these RNAs, it is possible toengineer molecules that recognize specific nucleotide sequences in anRNA molecule and cleave it (Cech, J. Amer. Med. Assn. 260:3030, 1988). Amajor advantage of this approach is that, because they aresequence-specific, only mRNAs with particular sequences are inactivated.

There are two basic types of ribozymes namely, tetrahymena-type(Hasselhoff, Nature 334:585, 1988) and “hammerhead”-type.Tetrahymena-type ribozymes recognize sequences which are four bases inlength, while “hammerhead”-type ribozymes recognize base sequences 11-18bases in length. The longer the recognition sequence, the greater thelikelihood that the sequence will occur exclusively in the target mRNAspecies. Consequently, hammerhead-type ribozymes are preferable totetrahymena-type ribozymes for inactivating a specific mRNA species and18-base recognition sequences are preferable to shorter recognitionsequences.

Various delivery systems are known and can be used to administer thesiRNAs and other inhibitory nucleic acid molecules as therapeutics. Suchsystems include, for example, encapsulation in liposomes,microparticles, microcapsules, nanoparticles, recombinant cells capableof expressing the therapeutic molecule(s) (see, e.g., Wu et al., J.Biol. Chem. 262, 4429, 1987), construction of a therapeutic nucleic acidas part of a retroviral or other vector, and the like.

C. Small Molecule Inhibitors

PD-1 antagonists include molecules that are identified from largelibraries of both natural product or synthetic (or semi-synthetic)extracts or chemical libraries according to methods known in the art.The screening methods that detect decreases in PD-1 activity (such asdetecting cell death) are useful for identifying compounds from avariety of sources for activity. The initial screens may be performedusing a diverse library of compounds, a variety of other compounds andcompound libraries. Thus, molecules that bind PD-1, PD-L1 or PD-L2,molecules that inhibit the expression of PD-1, PD-L1 and/or PD-L2, andmolecules that inhibit the activity of PD-1, PD-L1 and/or PD-L2 can beidentified. These small molecules can be identified from combinatoriallibraries, natural product libraries, or other small molecule libraries.In addition, PD-1 antagonist can be identified as compounds fromcommercial sources, as well as commercially available analogs ofidentified inhibitors.

The precise source of test extracts or compounds is not critical to theidentification of PD-1 antagonists. Accordingly, PD-1 antagonists can beidentified from virtually any number of chemical extracts or compounds.Examples of such extracts or compounds that can be PD-1 antagonistsinclude, but are not limited to, plant-, fungal-, prokaryotic- oranimal-based extracts, fermentation broths, and synthetic compounds, aswell as modification of existing compounds. Numerous methods are alsoavailable for generating random or directed synthesis (e.g.,semi-synthesis or total synthesis) of any number of chemical compounds,including, but not limited to, saccharide-, lipid-, peptide-, andnucleic acid-based compounds. Synthetic compound libraries arecommercially available from Brandon Associates (Merrimack, N.H.) andAldrich Chemical (Milwaukee, Wis.). PD-1 antagonists can be identifiedfrom synthetic compound libraries that are commercially available from anumber of companies including Maybridge Chemical Co. (Trevillet,Cornwall, UK), Comgenex (Princeton, N. J.), Brandon Associates(Merrimack, N.H.), and Microsource (New Milford, Conn.). PD-1antagonists can be identified from a rare chemical library, such as thelibrary that is available from Aldrich (Milwaukee, Wis.). PD-1antagonists can be identified in libraries of natural compounds in theform of bacterial, fungal, plant, and animal extracts are commerciallyavailable from a number of sources, including Biotics (Sussex, UK),Xenova (Slough, UK), Harbor Branch Oceangraphics Institute (Ft. Pierce,Fla.), and PharmaMar, U.S.A. (Cambridge, Mass.). Natural andsynthetically produced libraries and compounds are readily modifiedthrough conventional chemical, physical, and biochemical means.

Useful compounds may be found within numerous chemical classes, thoughtypically they are organic compounds, including small organic compounds.Small organic compounds have a molecular weight of more than 50 yet lessthan about 2,500 daltons, such as less than about 750 or less than about350 daltons can be utilized in the methods disclosed herein. Exemplaryclasses include heterocycles, peptides, saccharides, steroids, and thelike. The compounds may be modified to enhance efficacy, stability,pharmaceutical compatibility, and the like. In several embodiments,compounds of use has a Kd for PD-1, PD-L1 or PD-L2 of less than 1 nM,less than 10 nm, less than 1 μM, less than 10 μM, or less than 1 mM.

D. PD-1 Peptide Variants as Antagonists

In one embodiment, variants of a PD-1 protein which function as anantagonist can be identified by screening combinatorial libraries ofmutants, such as point mutants or truncation mutants, of a PD-1 proteinto identify proteins with antagonist activity. In one example, theantagonist is a soluble PD-1 protein.

Thus, a library of PD-1 variants can be generated by combinatorialmutagenesis at the nucleic acid level and is encoded by a variegatedgene library. A library of PD-1 variants can be produced by, forexample, by enzymatically ligating a mixture of syntheticoligonucleotides into gene sequences such that a degenerate set ofpotential PD-1 sequences is expressible as individual polypeptides, oralternatively, as a set of larger fusion proteins (such as for phagedisplay) containing the set of PD-1 sequences.

There are a variety of methods which can be used to produce libraries ofpotential PD-1 variants from a degenerate oligonucleotide sequence.Chemical synthesis of a degenerate gene sequence can be performed in anautomatic DNA synthesizer, and the synthetic gene then ligated into anappropriate expression vector. Use of a degenerate set of genes allowsfor the provision, in one mixture, of all of the sequences encoding thedesired set of potential PD-1 antagonist sequences. Methods forsynthesizing degenerate oligonucleotides are known in the art (see, forexample, Narang, et al., Tetrahedron 39:3, 1983; Itakura et al. Annu.Rev. Biochem. 53:323, 1984; Itakura et al. Science 198:1056, 1984).

In addition, libraries of fragments of a PD-1 protein coding sequencecan be used to generate a population of PD-1 fragments for screening andsubsequent selection of variants of a PD-1 antagonist. In oneembodiment, a library of coding sequence fragments can be generated bytreating a double stranded PCR fragment of a PD-1 coding sequence with anuclease under conditions wherein nicking occurs only about once permolecule, denaturing the double stranded DNA, renaturing the DNA to formdouble stranded DNA which can include sense/antisense pairs fromdifferent nicked products, removing single stranded portions fromreformed duplexes by treatment with Si nuclease, and ligating theresulting fragment library into an expression vector. By this method, anexpression library can be derived which encodes N-terminal, C-terminaland internal fragments of various sizes of PD-1.

Several techniques are known in the art for screening gene products ofcombinatorial libraries made by point mutations or truncation, and forscreening cDNA libraries for gene products having a selected property.Such techniques are adaptable for rapid screening of the gene librariesgenerated by the combinatorial mutagenesis of PD-1 proteins. The mostwidely used techniques, which are amenable to high through-put analysis,for screening large gene libraries typically include cloning the genelibrary into replicable expression vectors, transforming appropriatecells with the resulting library of vectors, and expressing thecombinatorial genes under conditions in which detection of a desiredactivity facilitates isolation of the vector encoding the gene whoseproduct was detected. Recursive ensemble mutagenesis (REM) can be usedin combination with the screening assays to identify PD-1 antagonists(Arkin and Youvan, Proc. Natl. Acad. Sci. USA 89:7811 7815, 1992;Delagrave et al., Protein Eng. 6(3):327 331, 1993).

In one embodiment, cell based assays can be exploited to analyze alibrary of PD-1 variants. For example, a library of expression vectorscan be transfected into a cell line which ordinarily synthesizes andsecretes PD-1. The transfected cells are then cultured such that PD-1and a particular PD-1 variant are secreted. The effect of expression ofthe mutant on PD-1 activity in cell supernatants can be detected, suchas by any of a functional assay. Plasmid DNA can then be recovered fromthe cells wherein endogenous PD-1 activity is inhibited, and theindividual clones further characterized.

Peptidomimetics can also be used as PD-1 antagonists. Peptide analogsare commonly used in the pharmaceutical industry as non-peptide drugswith properties analogous to those of the template peptide. These typesof non-peptide compounds and are usually developed with the aid ofcomputerized molecular modeling. Peptide mimetics that are structurallysimilar to therapeutically useful peptides can be used to produce anequivalent therapeutic or prophylactic effect. Generally,peptidomimetics are structurally similar to a paradigm polypeptide (forexample, polypeptide that has a PD-1 biological activity), but has oneor more peptide linkages optionally replaced by a —CH₂NH—, —CH₂S—,—CH₂—CH₂—, —CH.═.CH— (cis and trans), —COCH₂—, —CH(OH)CH₂—, and —CH₂SO—linkages. These peptide linkages can be replaced by methods known in theart (see, for example, Morley, Trends Pharm. Sci. pp. 463 468, 1980;Hudson et al. Int. J. Pept. Prot. Res. 14:177 185, 1979; Spatola, LifeSci. 38:1243 1249, 1986; Holladay, et al. Tetrahedron Lett. 24:44014404, 1983). Peptide mimetics can be procured economically, be stable,and can have increased half-life or absorption. Labeling ofpeptidomimetics usually involves covalent attachment of one or morelabels, directly or through a spacer (such as by an amide group), tonon-interfering position(s) on the peptidomimetic that are predicted byquantitative structure-activity data and/or molecular modeling. Suchnon-interfering positions generally are positions that do not formdirect contacts with the macromolecules(s) to which the peptidomimeticbinds to produce the therapeutic effect. Derivitization ofpeptidomimetics should not substantially interfere with the desiredbiological or pharmacological activity of the peptidomimetic.

A dominant negative protein or a nucleic acid encoding a dominantnegative protein that interferes with the biological activity of PD-1(i.e. binding of PD-1 to PD-L1, PD-L2, or both) can also be used in themethods disclosed herein. A dominant negative protein is any amino acidmolecule having a sequence that has at least 50%, 70%, 80%, 90%, 95%, oreven 99% sequence identity to at least 10, 20, 35, 50, 100, or more than150 amino acids of the wild type protein to which the dominant negativeprotein corresponds. For example, a dominant-negative PD-L1 has mutationsuch that it binds PD-1 more tightly than native (wild-type) PD-1 butdoes not activate any cellular signaling through PD-1.

The dominant negative protein may be administered as an expressionvector. The expression vector may be a non-viral vector or a viralvector (e.g., retrovirus, recombinant adeno-associated virus, or arecombinant adenoviral vector). Alternatively, the dominant negativeprotein may be directly administered as a recombinant proteinsystemically or to the infected area using, for example, microinjectiontechniques.

Polypeptide antagonists can be produced in prokaryotic or eukaryotichost cells by expression of polynucleotides encoding the amino acidsequence, frequently as part of a larger polypeptide (a fusion protein,such as with ras or an enzyme). Alternatively, such peptides can besynthesized by chemical methods. Methods for expression of heterologousproteins in recombinant hosts, chemical synthesis of polypeptides, andin vitro translation are well known in the art (see Maniatis el al.Molecular Cloning: A Laboratory Manual (1989), 2nd Ed., Cold SpringHarbor, N.Y.; Berger and Kimmel, Methods in Enzymology, Volume 152,Guide to Molecular Cloning Techniques (1987), Academic Press, Inc., SanDiego, Calif.; Kaiser et al., Science 243:187, 1989; Merrifield, Science232:342, 1986; Kent, Annu. Rev. Biochem. 57:957, 1988).

Peptides can be produced, such as by direct chemical synthesis, and usedas antagonists of a PD-1 interaction with a ligand. Peptides can beproduced as modified peptides, with nonpeptide moieties attached bycovalent linkage to the N-terminus and/or C-terminus. In certainpreferred embodiments, either the carboxy-terminus or theamino-terminus, or both, are chemically modified. The most commonmodifications of the terminal amino and carboxyl groups are acetylationand amidation, respectively Amino-terminal modifications such asacylation (for example, acetylation) or alkylation (for example,methylation) and carboxy-terminal-modifications such as amidation, aswell as other terminal modifications, including cyclization, can beincorporated into various embodiments. Certain amino-terminal and/orcarboxy-terminal modifications and/or peptide extensions to the coresequence can provide advantageous physical, chemical, biochemical, andpharmacological properties, such as: enhanced stability, increasedpotency and/or efficacy, resistance to serum proteases, desirablepharmacokinetic properties, and others.

Method of Treatment: Administration of a PD-1 Antagonist to a Subject

Methods are provided herein to treat a variety of infections andcancers. In these methods, the infection or cancer is treated, preventedor a symptom is alleviated by administering to a subject atherapeutically effective amount of a PD-1 antagonist. The subject canbe any mammal such as human, a primate, mouse, rat, dog, cat, cow,horse, and pig. In several examples, the subject is a primate, such as ahuman. In additional examples, the subject is a murine subject, such asa mouse. In some embodiments, the method includes measuring memory Bcell proliferation in a sample from the subject (see below). In someexamples, the methods also include measuring naïve B cells in a samplefrom the subject. In additional examples, the methods include measure Tcells that express CD28 (CD28+) cells.

In several embodiments, the subject is at risk of developing infection.A subject at risk of developing infection is a subject that does not yethave the infection, but can be infected by the infectious agent ofinterest. In additional examples, the subject has an infection, such asa persistent infection, for example a chronic infection. A subject witha persistent infection, such as a chronic infection, can be identifiedby standard methods suitable by one of skill in the art, such as aphysician.

In several examples, the subject has a persistent infection with abacteria virus, fungus, or parasite. Generally, persistent infections,in contrast to acute infections are not effectively cleared by theinduction of a host immune response. The infectious agent and the immuneresponse reach equilibrium such that the infected subject remainsinfectious over a long period of time without necessarily expressingsymptoms. Persistent infections include for example, latent, chronic andslow infections. Persistent infection occurs with viruses such as humanT-Cell leukemia viruses, Epstein-Barr virus, cytomegalovirus,herpesviruses, varicella-zoster virus, measles, papovaviruses, prions,hepatitis viruses, adenoviruses, XMRV, polyoma JC virus, parvovirusesand papillomaviruses.

In a chronic infection, the infectious agent can be detected in the bodyat all times. However, the signs and symptoms of the disease may bepresent or absent for an extended period of time. Examples of chronicinfection include hepatitis B (caused by heptatitis B virus (HBV)) andhepatitis C (caused by hepatitis C virus (HCV)) adenovirus,cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1, herpessimplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitisB virus, hepatitis D virus, papilloma virus, parvovirus B19,polyomavirus K, polyomavirus JC, XMRV, measles virus, rubella virus,human immunodeficiency virus (HIV), human T cell leukemia virus I, andhuman T cell leukemia virus II. Parasitic persistent infections mayarise as a result of infection by Leishmania, Toxoplasma, Trypanosoma,Plasmodium, Schistosoma, and Encephalitozoon.

In a latent infection, the infectious agent (such as a virus) isseemingly inactive and dormant such that the subject does always exhibitsigns or symptoms. In a latent viral infection, the virus remains inequilibrium with the host for long periods of time before symptoms againappear; however, the actual viruses cannot be detected untilreactivation of the disease occurs. Examples of latent infectionsinclude infections caused by herpes simplex virus (HSV)-1 (feverblisters), HSV-2 (genital herpes), and varicella zoster virus VZV(chickenpox-shingles).

In a slow infection, the infectious agents gradually increase in numberover a very long period of time during which no significant signs orsymptoms are observed. Examples of slow infections include AIDS (causedby HIV-1 and HIV-2), lentiviruses that cause tumors in animals, andprions.

In addition, persistent infections often arise as late complications ofacute infections. For example, subacute sclerosing panencephalitis(SSPE) can occur following an acute measles infection or regressiveencephalitis can occur as a result of a rubella infection.

In one non-limiting example, a subject may be diagnosed as having apersistent Chlamydial infection following the detection of Chlamydialspecies in a biological sample from this individual using PCR analysis.Mammals need not have not been diagnosed with a persistent infection tobe treated according to this disclosure. Microbial agents capable ofestablishing a persistent infection include viruses (such as papillomavirus, hepatitis virus, human immune deficiency virus, and herpesvirus), bacteria (such as Escherichia coli and Chlamydia spp.),parasites, (such as Leishmania spp., Schistosoma spp., Trypanosoma spp.,Toxoplasma spp.) and fungi.

In addition to the compound that reduces PD-1 expression or activity,the subject being treated may also be administered a vaccine. In oneexample, the vaccine can include an adjuvant. In another example, thevaccine can include a prime booster immunization. The vaccine can be aheat-killed vaccine, an attenuated vaccine, or a subunit vaccine. Asubject already infected with a pathogen can be treated with atherapeutic vaccine, such as a PD-1 antagonist and an antigen. Thesubject can be asymptomatic, so that the treatment prevents thedevelopment of a symptom. The therapeutic vaccine can also reduce theseverity of one or more existing symptoms, or reduce pathogen load.

In several examples of treatment methods, the subject is administered atherapeutically effective amount of a PD-1 antagonist in conjunctionwith a viral antigen. Non-limiting examples of suitable viral antigensinclude: influenza HA, NA, M, NP and NS antigens; HIV p24, pol, gp41 andgp120; Metapneumovirus (hMNV) F and G proteins; Hepatitis C virus (HCV)E1, E2 and core proteins; Dengue virus (DEN1-4) E1, E2 and coreproteins; Human Papilloma Virus L1 protein; Epstein Barr Virus gp220/350and EBNA-3A peptide; Cytomegalovirus (CMV) gB glycoprotein, gHglycoprotein, pp65, IE1 (exon 4) and pp150; Varicella Zoster virus (VZV)1E62 peptide and glycoprotein E epitopes; Herpes Simplex VirusGlycoprotein D epitopes, polyoma JC virus polypeptides, XMRVpolypeptides, among many others. The antigenic polypeptides cancorrespond to polypeptides of naturally occurring animal or human viralisolates, or can be engineered to incorporate one or more amino acidsubstitutions as compared to a natural (pathogenic or non-pathogenic)isolate. Exemplary antigens are listed below:

TABLE 1  Exemplary antigens of interest (target antigens)Exemplary Antigen  SEQ Sequences from the  ID Antigens of interest NO:Viral Antigens BK TLYKKMEQDVKVAHQ 13 GNLPLMRKAYLRKCK 14 TFSRMKYNICMGKCI15 JC SITEVECFL 16 Epstein-Barr QPRAPIRPI 17 (EBV) cytomegalovirusNLVPMVATV 18 (CMV) HPV YMLDLQPET(T) 19 Influenza A GILGFVFTL 20Fungal Antigen Blastomyces CELDNSHEDYNWNLWFKWCSGHGR 47 dermatitidisTGHGKHFYDCDWDPSHGDYSWYLW 48 DPSHGDYSWYLWDYLCGNGHHPYD 49DYLCGNGHHPYDCELDNSHEDYSW 50 DPYNCDWDPYHEKYDWDLWNKWCN 51KYDWDLWNKWCNKDPYNCDWDPYH 52

In additional embodiments, the subject has a tumor. The method includesadministering to the subject a therapeutically effective amount of aPD-1 antagonist, thereby treating the tumor. In several examples, atherapeutically effective amount of a tumor antigen, or a nucleotideencoding the tumor antigen, is also administered to the subject. ThePD-1 antagonist and the tumor antigen, or nucleotide encoding the tumorantigen, can be administered simultaneously or sequentially.

Administration of the PD-1 antagonist results in a decrease in size,prevalence, or metastatic potential of a tumor in a subject. Assessmentof cancer is made using standard clinical protocols. Efficacy isdetermined in association with any known method for diagnosing ortreating the particular tumor.

Tumors (also called “cancers”) include solid tumors and leukemias.Exemplary tumors include those listed in table 2 (along with known tumorantigens associated with these cancers).

TABLE 2  Exemplary tumors and their tumor antigens Tumor Tumor AntigensAcute myelogenous Wilms tumor 1 (WT1),  leukemiapreferentially expressed antigen of melanoma (PRAME),PR1, proteinase 3, elastase, cathepsin G Chronic myelogenousWT1, PRAME, PR1, proteinase leukemia 3, elastase, cathepsin GMyelodysplastic  WT1, PRAME, PR1, proteinase syndrome3, elastase, cathepsin G Acute lymphoblastic  PRAME leukemiaChronic lymphocytic  Survivin leukemia Non-Hodgkin's lymphoma SurvivinMultiple myeloma New York esophageous 1 (NY-Eso1) Malignant melanomaMAGE, MART, Tyrosinase, PRAME, GP100 Breast cancer WT1, herceptinLung cancer WT1 Prostate cancer Prostate-specific antigen (PSA)Colon cancer Carcinoembryonic antigen (CEA) Renal cell carcinomaFibroblast growth factor 5 (RCC) (FGF-5)

TABLE 3  Exemplary tumor antigens of interest include those listed belowTumor Antigens and their derivative peptides PRAME LYVDSLFFL 21 WT1RMFPNAPYL 22 Survivin ELTLGEFLKL 23 AFP GVALQTMKQ 24 ELF2M ETVSEQSNV 25proteinase 3 and its VLQELNVTV 26 peptide PR1 neutrophil elastaseVLQELNVTV 27 MAGE EADPTGHSY 28 MART AAGIGILTV 29 tyrosinaseRHRPLQEVYPEANAPI 30 GHNRE GP100 WNRQLYPEWTEAQRLD 31 NY-Eso-1 VLLKEFTVSG32 Herceptin KIFGSLAFL 33 carcino-embryonic  HLFGYSWYK 34 antigen (CEA)PSA FLTPKKLQCV 35

Specific non-limiting examples are angioimmunoblastic lymphoma ornodular lymphocyte predominant Hodgkin lymphoma. Angioimmunoblasticlymphoma (AIL) is an aggressive (rapidly progressing) type of T-cellnon-Hodgkin lymphoma marked by enlarged lymph nodes andhypergammaglobulinemia (increased antibodies in the blood). Othersymptoms may include a skin rash, fever, weight loss, positive Coomb'stest or night sweats. This malignancy usually occurs in adults. Patientsare usually aged 40-90 years (median around 65) and are more often male.As AIL progresses, hepatosplenomegaly, hemolytic anemia, and polyclonalhypergammaglobulinemia may develop. The skin is involved inapproximately 40-50% of patients.

Nodular lymphocyte predominant Hodgkin lymphoma is a B cell neoplasmthat appears to be derived from germinal center B cells with mutated,non-functional immunoglobulin genes. Similar to angioimmunoblasticlymphoma, neoplastic cells are associated with a meshwork of folliculardendritic cells. PD-1 expression is seen in T cells closely associatedwith neoplastic CD20+ cell in nodular lymphocyte predominant Hodgkinlymphoma, in a pattern similar to that seen for CD57+ T cells. CD57 hasbeen identified as another marker of germinal center-associated T cells,along with CXCR5, findings which support the conclusion that theneoplastic cells in nodular lymphocyte predominant Hodgkin lymphoma havea close association with germinal center-associated T cells.

Expression of a tumor antigen of interest can be determined at theprotein or nucleic acid level using any method known in the art. Forexample, Northern hybridization analysis using probes which specificallyrecognize one or more of these sequences can be used to determine geneexpression. Alternatively, expression is measured usingreverse-transcription-based PCR assays, such as using primers specificfor the differentially expressed sequence of genes. Expression is alsodetermined at the protein level, such as by measuring the levels ofpeptides encoded by the gene products described herein, or activitiesthereof. Such methods are well known in the art and include, for exampleimmunoassays based on antibodies to proteins encoded by the genes. Anybiological material can be used for the detection/quantification of theprotein or the activity.

In one example, the subject has been previously diagnosed as havingcancer. In additional examples, the subject has undergone priortreatment for the cancer. However, in some examples, the subject has notbeen previously diagnosed as having the cancer. Diagnosis of a solidtumor can be made through the identification of a mass on anexamination, although it may also be through other means such as aradiological diagnosis, or ultrasound. Treatment of cancer can includesurgery, or can include the use of chemotherapeutic agents Such asdocetaxel, vinorelbine gemcitabine, capecitabine or combinations ofcyclophosphamide, methotrexate, and fluorouracil; cyclophosphamide,doxorubicin, and fluorouracil; doxorubicin and cyclophosphamide;doxorubicin and cyclophosphamide with paclitaxel; doxorubicin followedby CMF (Cyclophosphamide, epirubicin and fluorouracil). In addition,treatment can include the use of radiation.

In several examples, a therapeutically effective amount a PD-1antagonist is administered to the subject. A therapeutically effectiveamount of a tumor antigen, or a nucleic acid encoding the antigen, isalso administered to the subject. The administration can be concurrentor can be sequential.

For the treatment of a subject with a persistent infection (such as achronic infection) or a tumor, a therapeutically effective amount of aPD-1 antagonist is administered to the subject of interest. In oneexample, a therapeutically effective amount of a PD-1 antagonist is abiologically active dose, such as a dose that will induce an increase inCD8+ T cell cytotoxic activity the increase in the immune responsespecific to the infectious agent. Desirably, the PD-1 antagonist has theability to reduce the expression or activity of PD-1 in antigen specificimmune cells (e.g., T cells such as CD8+ T cells) by at least 5%, 10%,20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more than 100% belowuntreated control levels. The levels or activity of PD-1 in immune cellsis measured by any method known in the art, including, for example,Western blot analysis, immunohistochemistry, ELISA, and Northern Blotanalysis. Alternatively, the biological activity of PD-1 is measured byassessing binding of PD-1 to PD-L1, PD-L2, or both. The biologicalactivity of PD-1 is determined according to its ability to increase CD8+T cell cytotoxicity including, for example, cytokine production,clearance of the infectious agent, and proliferation of antigen specificCD8+ T cells. Preferably, the agent that reduces the expression oractivity of PD-1 can increase the immune response specific to theinfectious agent or the tumor by at least 5%, 10%, 20%, 30%, 40%, 50%,60%, 70%, 80%, 90%, or more than 100% above untreated control levels.The agent of the present invention is therefore any agent having any oneor more of these activities. Although the agent is preferably expressedin CD8+ T cells, it is understood that any cell that can influence theimmune response to persistent infections is also amenable to the methodsof the invention and include, for example, B cells.

Optionally, the subject is administered one or more additionaltherapeutic agents. Additional therapeutic agents include, for example,antiviral compounds (e.g., vidarabine, acyclovir, gancyclovir,valgancyclovir, nucleoside-analog reverse transcriptase inhibitor (NRTI)(e.g., AZT (Zidovudine), ddI (Didanosine), ddC (Zalcitabine), d4T(Stavudine), or 3TC (Lamivudine)), non-nucleoside reverse transcriptaseinhibitor (NNRTI) (e.g., (nevirapine or delavirdine), protease inhibitor(saquinavir, ritonavir, indinavir, or nelfinavir), ribavirin, orinterferon), antibacterial compounds, antifungal compounds,antiparasitic compounds, anti-inflammatory compounds, anti-neoplasticagent (chemotherapeutics) or analgesics.

The additional therapeutic agent is administered prior to,concomitantly, or subsequent to administration of the PD-1 antagonist.For example, the PD-1 antagonist and the additional agent areadministered in separate formulations within at least 1, 2, 4, 6, 10,12, 18, or more than 24 hours apart. Optionally, the additional agent isformulated together with the PD-1 antagonist. When the additional agentis present in a different composition, different routes ofadministration may be used. The agent is administered at doses known tobe effective for such agent for treating, reducing, or preventing aninfection.

Concentrations of the PD-1 antagonist and the additional agent dependsupon different factors, including means of administration, target site,physiological state of the mammal, and other medication administered.Thus treatment dosages may be titrated to optimize safety and efficacyand is within the skill of an artisan. Determination of the properdosage and administration regime for a particular situation is withinthe skill of the art.

Optionally, the subject is further administered a vaccine that elicits aprotective immune response against the infectious agent that causes apersistent infection. For example, the subject receives a vaccine thatelicits an immune response against human immunodeficiency virus (HIV),tuberculosis, influenza, XMRV, polyoma JC virus, or hepatitis C, amongstothers. Exemplary vaccines are described, for example, in Berzofsky etal. (J. Clin. Invest. 114:456-462, 2004). If desired, the vaccine isadministered with a prime-booster shot or with adjuvants. The vaccinecan also be a tumor vaccine, such as a therapeutically effective amountof a tumor antigen. In several embodiments, a therapeutically effectiveamount of an antigenic polypeptide, such as a viral or a tumor antigen,is administered to the subject.

A therapeutically effective amount of the tumor antigen, or a nucleicacid encoding the tumor antigen can be administered to the subject. Thepolynucleotides include a recombinant DNA which is incorporated into avector into an autonomously replicating plasmid or virus or into thegenomic DNA of a prokaryote or eukaryote, or which exists as a separatemolecule (such as a cDNA) independent of other sequences. Thenucleotides be ribonucleotides, deoxyribonucleotides, or modified formsof either nucleotide. The term includes single and double forms of DNA.

A number of viral vectors have been constructed, including polyoma,i.e., SV40 (Madzak et al., 1992, J. Gen. Virol., 73:15331536),adenovirus (Berkner, 1992, Cur. Top. Microbiol. Immunol., 158:39-6;Berliner et al., 1988, Bio Techniques, 6:616-629; Gorziglia et al.,1992, J. Virol., 66:4407-4412; Quantin et al., 1992, Proc. Nad. Acad.Sci. USA, 89:2581-2584; Rosenfeld et al., 1992, Cell, 68:143-155;Wilkinson et al., 1992, Nucl. Acids Res., 20:2233-2239;Stratford-Perricaudet et al., 1990, Hum. Gene Ther., 1:241-256),vaccinia virus (Mackett et al., 1992, Biotechnology, 24:495-499),adeno-associated virus (Muzyczka, 1992, Curr. Top. Microbiol. Immunol.,158:91-123; On et al., 1990, Gene, 89:279-282), herpes viruses includingHSV and EBV (Margolskee, 1992, Curr. Top. Microbiol. Immunol.,158:67-90; Johnson et al., 1992, J. Virol., 66:29522965; Fink et al.,1992, Hum. Gene Ther. 3:11-19; Breakfield et al., 1987, Mol. Neurobiol.,1:337-371; Fresse et al., 1990, Biochem. Pharmacol., 40:2189-2199),Sindbis viruses (H. Herweijer et al., 1995, Human Gene Therapy6:1161-1167; U.S. Pat. Nos. 5,091,309 and 5,2217,879), alphaviruses (S.Schlesinger, 1993, Trends Biotechnol. 11:18-22; I. Frolov et al., 1996,Proc. Natl. Acad. Sci. USA 93:11371-11377) and retroviruses of avian(Brandyopadhyay et al., 1984, Mol. Cell Biol., 4:749-754; Petropouploset al., 1992, J. Virol., 66:3391-3397), murine (Miller, 1992, Curr. Top.Microbiol. Immunol., 158:1-24; Miller et al., 1985, Mol. Cell Biol.,5:431-437; Sorge et al., 1984, Mol. Cell Biol., 4:1730-1737; Mann etal., 1985, J. Virol., 54:401-407), and human origin (Page et al., 1990,J. Virol., 64:5370-5276; Buchschalcher et al., 1992, J. Virol.,66:2731-2739). Baculovirus (Autographa californica multinuclearpolyhedrosis virus; AcMNPV) vectors are also known in the art, and maybe obtained from commercial sources (such as PharMingen, San Diego,Calif.; Protein Sciences Corp., Meriden, Conn.; Stratagene, La Jolla,Calif.).

In one embodiment, the polynucleotide encoding a tumor antigen or aviral antigen is included in a viral vector. Suitable vectors includeretrovirus vectors, orthopox vectors, avipox vectors, fowlpox vectors,capripox vectors, suipox vectors, adenoviral vectors, herpes virusvectors, alpha virus vectors, baculovirus vectors, Sindbis virusvectors, vaccinia virus vectors and poliovirus vectors. Specificexemplary vectors are poxvirus vectors such as vaccinia virus, fowlpoxvirus and a highly attenuated vaccinia virus (MVA), adenovirus,baculovirus and the like.

Pox viruses of use include orthopox, suipox, avipox, and capripox virus.Orthopox include vaccinia, ectromelia, and raccoon pox. One example ofan orthopox of use is vaccinia. Avipox includes fowlpox, canary pox andpigeon pox. Capripox include goatpox and sheeppox. In one example, thesuipox is swinepox. Examples of pox viral vectors for expression asdescribed for example, in U.S. Pat. No. 6,165,460, which is incorporatedherein by reference. Other viral vectors that can be used include otherDNA viruses such as herpes virus and adenoviruses, and RNA viruses suchas retroviruses and polio.

In several embodiments, PD-1 antagonists are administered in an amountsufficient to increase T cell, such as CD8+ T cell, cytotoxicity. Anincrease in T-cell cytotoxicity results in an increased immune responseand a reduction in the persistent infection, or a reduction in a sign ora symptom of a tumor. An increased immune response can be measured, forexample, by an increase in immune cell proliferation, such as T-cell orB cell proliferation, an increase in cytokine production, and anincrease in the clearance of an infectious agent or a reduction in tumorburden. Thus, the method can result in alleviation of one or more ofsymptoms associated with the persistent infection or tumor. Thus,administration of the PD-1 antagonist reduces the persistent infection,inhibits the growth/size of a tumor, or alleviates one or more symptomsassociated with the persistent infection or tumor by at least 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% as compared to an untreatedsubject.

Treatment is efficacious if the treatment leads to clinical benefit suchas, a reduction of the load of the infectious agent or a reduction oftumor burden in the subject. When treatment is applied prophylactically,“efficacious” means that the treatment retards or prevents an infectionfrom forming, such as for a period of six months, one year, two years,three years or more. Efficacy may be determined using any known methodfor diagnosing or treating the particular infection or tumor.

Thus, the methods include administering to a subject a pharmaceuticalcomposition that includes a therapeutically effective amount of a PD-1antagonist. An effective amount of a therapeutic compound, such as anantibody, can be for example from about 0.1 mg/kg to about 150 mg/kg.Effective doses vary, as recognized by those skilled in the art,depending on route of administration, excipient usage, andcoadministration with other therapeutic treatments including use ofother anti-infection agents or therapeutic agents for treating,preventing or alleviating a symptom of a particular infection or cancer.A therapeutic regimen is utilized for a human patient suffering from (orat risk of developing) an infection or cancer, using standard methods.

The PD-1 antagonist is administered to such an individual using methodsknown in the art. Any PD-1 antagonist can be utilized, such as thosedisclosed herein. In addition, more than one PD-1 antagonist can beutilized. A PD-1 antagonist can be administered locally or systemically.For example, the PD-1 antagonist is administered orally, rectally,nasally, topically parenterally, subcutaneously, intraperitoneally,intramuscularly, and intravenously. The PD-1 antagonist can beadministered prophylactically, or after the detection of an infection ortumor. The PD-1 antagonist is optionally formulated as a component of acocktail of therapeutic drugs to treat infection. Examples offormulations suitable for parenteral administration include aqueoussolutions of the active agent in an isotonic saline solution, a 5%glucose solution, or another standard pharmaceutically acceptableexcipient. Standard solubilizing agents such as PVP or cyclodextrins arealso utilized as pharmaceutical excipients for delivery of thetherapeutic compounds.

The therapeutic compounds described herein are formulated intocompositions for other routes of administration utilizing conventionalmethods. For example, PD-1 antagonist is formulated in a capsule or atablet for oral administration. Capsules may contain any standardpharmaceutically acceptable materials such as gelatin or cellulose.Tablets may be formulated in accordance with conventional procedures bycompressing mixtures of a therapeutic compound with a solid carrier anda lubricant. Examples of solid carriers include starch and sugarbentonite. The PD-1 antagonist can be administered in the form of a hardshell tablet or a capsule containing a binder, such as lactose ormannitol, a conventional filler, and a tableting agent. Otherformulations include an ointment, suppository, paste, spray, patch,cream, gel, resorbable sponge, or foam. Such formulations are producedusing methods well known in the art.

Additionally, PD-1 antagonists can be administered by implanting (eitherdirectly into an organ (e.g., intestine or liver) or subcutaneously) asolid or resorbable matrix which slowly releases the compound intoadjacent and surrounding tissues of the subject. For example, for thetreatment of gastrointestinal infection, the compound may beadministered systemically (e.g., intravenously, rectally or orally) orlocally (e.g., directly into gastric tissue). Alternatively, a PD-1antagonist-impregnated wafer or resorbable sponge is placed in directcontact with gastric tissue. The PD-1 antagonist is slowly released invivo by diffusion of the drug from the wafer and erosion of the polymermatrix. As another example, infection of the liver (i.e., hepatitis) istreated by infusing into the liver vasculature a solution containing thePD-1 antagonist.

Where the therapeutic compound is a nucleic acid encoding a PD-1antagonist, the nucleic acid can be administered in vivo to promoteexpression of the encoded protein, by constructing it as part of anappropriate nucleic acid expression vector and administering it so thatit becomes intracellular (such by use of a retroviral vector, by directinjection, by use of microparticle bombardment, by coating with lipidsor cell-surface receptors or transfecting agents, or by administering itin linkage to a homeobox-like peptide which is known to enter thenucleus (See, e.g., Joliot, et al., Proc Natl Acad Sci USA 88:1864-1868,1991), and the like. Alternatively, a nucleic acid therapeutic isintroduced intracellularly and incorporated within host cell DNA forexpression, by homologous recombination or remain episomal.

For local administration of DNA, standard gene therapy vectors can beused. Such vectors include viral vectors, including those derived fromreplication-defective hepatitis viruses (such as HBV and HCV),retroviruses (see, PCT Publication No. WO 89/07136; Rosenberg et al., N.Eng. J. Med. 323(9):570-578, 1990, adenovirus (see, Morsey et al., J.Cell. Biochem., Supp. 17E, 1993), adeno-associated virus (Kotin et al.,Proc. Natl. Acad. Sci. USA 87:2211-2215, 1990), replication defectiveherpes simplex viruses (HSV; Lu et al., Abstract, page 66, Abstracts ofthe Meeting on Gene Therapy, September 22-26, Cold Spring HarborLaboratory, Cold Spring Harbor, N.Y., 1992, and any modified versions ofthese vectors. Any other delivery system can be utilized thataccomplishes in vivo transfer of nucleic acids into eukaryotic cells.For example, the nucleic acids may be packaged into liposomes, such ascationic liposomes (Lipofectin), receptor-mediated delivery systems,non-viral nucleic acid-based vectors, erythrocyte ghosts, ormicrospheres (such as microparticles; see, e.g., U.S. Pat. No.4,789,734; U.S. Pat. No. 4,925,673; U.S. Pat. No. 3,625,214). Naked DNAmay also be administered.

With regard to nucleic acid inhibitors, a therapeutically effectiveamount is an amount which is capable of producing a medically desirableresult, e.g., a decrease of a PD-1 gene product in a treated animal.Such an amount can be determined by one of ordinary skill in the art.Dosage for any given patient depends upon many factors, including thepatient's size, body surface area, age, the particular compound to beadministered, sex, time and route of administration, general health, andother drugs being administered concurrently. Dosages may vary, but apreferred dosage for intravenous administration of DNA is approximately106 to 1022 copies of the DNA molecule.

Typically, plasmids are administered to a mammal in an amount of about 1nanogram to about 5000 micrograms of DNA. Desirably, compositionscontain about 5 nanograms to 1000 micrograms of DNA, 10 nanograms to 800micrograms of DNA, 0.1 micrograms to 500 micrograms of DNA, 1 microgramto 350 micrograms of DNA, 25 micrograms to 250 micrograms of DNA, or 100micrograms to 200 micrograms of DNA. Alternatively, administration ofrecombinant adenoviral vectors encoding the PD-1 antagonist into amammal may be administered at a concentration of at least 105, 106, 107,108, 109, 1010, or 1011 plaque forming unit (pfu).

In some embodiments, for the treatment of neurological infections, thePD-1 antagonist can be administered intravenously or intrathecally (forexample, by direct infusion into the cerebrospinal fluid). For localadministration, a compound-impregnated wafer or resorbable sponge isplaced in direct contact with central nervous system (CNS) tissue. Thecompound or mixture of compounds is slowly released in vivo by diffusionof the drug from the wafer and erosion of the polymer matrix.Alternatively, the compound is infused into the brain or cerebrospinalfluid using standard methods. For example, a burr hole ring with acatheter for use as an injection port is positioned to engage the skullat a burr hole drilled into the skull. A fluid reservoir connected tothe catheter is accessed by a needle or stylet inserted through a septumpositioned over the top of the burr hole ring. A catheter assembly(described, for example, in U.S. Pat. No. 5,954,687) provides a fluidflow path suitable for the transfer of fluids to or from selectedlocation at, near or within the brain to allow administration of thedrug over a period of time.

In additional embodiments, for cardiac infections, the PD-1 antagonistcan be delivered, for example, to the cardiac tissue (such as themyocardium, pericardium, or endocardium) by direct intracoronaryinjection through the chest wall or using standard percutaneous catheterbased methods under fluoroscopic guidance. Thus, the PD-1 antagonist maybe directly injected into tissue or may be infused from a stent orcatheter which is inserted into a bodily lumen. Any variety of coronarycatheter or perfusion catheter may be used to administer the compound.Alternatively, the PD-1 antagonist is coated or impregnated on a stentthat is placed in a coronary vessel.

Pulmonary infections can be treated, for example, by administering thePD-1 antagonist by inhalation. The compounds are delivered in the formof an aerosol spray from a pressured container or dispenser whichcontains a suitable propellant, such as a gas such as carbon dioxide ora nebulizer.

One in the art will understand that the patients treated can have beensubjected to the same tests to diagnose a persistently infected subjector may have been identified, without examination, as one at high riskdue to the presence of one or more risk factors (such as exposure toinfectious agent, exposure to infected subject, genetic predisposition,or having a pathological condition predisposing to secondaryinfections). Reduction of persistent infection symptoms or damage mayalso include, but are not limited to, alleviation of symptoms,diminishment of extent of disease, stabilization (not worsening) stateof disease, delay or slowing of disease progression, and amelioration orpalliation of the disease state. Treatment can occur at home with closesupervision by the health care provider, or can occur in a health carefacility.

Methods for measuring the immune response following treatment using themethods disclosed herein are well known in the art. The activity of Tcells may be assessed, for example, by assays that detect cytokineproduction, assays measuring T cell proliferation, assays that measurethe clearance of the microbial agent, and assays that measure CD8+ Tcell cytotoxicity. These assays are described, for example, in U.S. Pat.No. 6,808,710 and U.S. Patent Application Publication Nos. 20040137577,20030232323, 20030166531, 20030064380, 20030044768, 20030039653,20020164600, 20020160000, 20020110836, 20020107363, and 20020106730, allof which are hereby incorporated by reference. The measurement of a Bcell response, such as a memory B cell response, is described below.

Optionally, the ability of a PD-1 antagonist to increase CD8+ T cellcytotoxicity is assessed by assays that measure the proliferation ofCD8+ T cells (for example, thymidine incorporation, BrdU assays, andstaining with cell cycle markers (for example, Ki67 and CFSE),described, for example, by Dong et al. (Nature 5:1365-1369, 1999). Inone example, T-cell proliferation is monitored by culturing the purifiedT-cells expressing PD-1 with a PD-1 antagonist, a primary activationsignal as described above, and ³H-thymidine. The level of T-cellproliferation is determined by measuring thymidine incorporation. CD8+ Tcell cytotoxicity also can be assessed by lysis assays (such as ⁵¹Crrelease assays or assays detecting the release of perforin or granzyme),assays that detect caspase activation, or assays that measure theclearance of the microbial agent from the infected subject. For example,the viral load in a biological sample from the infected subject (e.g.,serum, spleen, liver, lung, or the tissue to which the virus is tropic)may be measured before and after treatment.

The production of cytokines such as IFNγ, TNF-α, and IL-2 may also bemeasured. For example, purified T-cells are cultured in the presence ofthe PD-1 protein antagonist and a primary activation signal. The levelof various cytokines in the supernatant can be determined by sandwichenzyme-linked immunosorbent assays or other conventional assaysdescribed, for example, in Dong et al. (Nature 5:1365-1369, 1999).

If desired, the efficacy of the PD-1 antagonist is assessed by itsability to induce co-stimulation of T cells. For example, a method forin vitro T-cell co-stimulation involves providing purified T-cells thatexpress PD-1 with a first or primary activation signal by anti-CD3monoclonal antibody or phorbol ester, or by antigen in association withclass II MHC. The ability of a candidate compound agent to reduce PD-1expression or activity and therefore provide the secondary orco-stimulatory signal necessary to modulate immune function, to theseT-cells can then be assayed by any one of the several conventionalassays well known in the art.

The B cell response to the PD-1 antagonist can be assessed by LCMVspecific ELISA, plasma cell ELISPOT, memory B-cell assay, phenotyping ofB cell, and analysis of germinal centers by immunohistochemistry.

Methods of Treatment: Adoptive Immunotherapy

Methods are disclosed herein for the treatment of a subject of interest,such as a subject with a persistent viral infection (such as a chronicinfection) or a tumor. The methods include the administration of atherapeutically effective amount of cytoxic T cells specific for anantigen of interest, such as a viral antigen or a tumor antigen, and atherapeutically effective amount of a PD-1 antagonist. In someembodiments, the method can also include measuring memory B cellproliferation in a sample from the subject (see below). In additionalembodiments, the methods include measuring naïve B cells in a samplefrom the subject. In further embodiments, the methods also includemeasuring T cells that express CD28. In some embodiments, the methodsinclude measuring neutralizing antibodies. Thus, the disclosed methodsinclude measuring at least one of neutralizing antibodies, memory B cellproliferation, naïve B cells, and T cells that express CD28. Two, threeor all of these parameters can be measured using the methods disclosedherein.

Methods are disclosed herein for increasing the immune response, such asenhancing the immune system in a subject. Administration of the purifiedantigen-specific T cells and PD-1, as disclosed herein, will increasethe ability of a subject to overcome pathological conditions, such as aninfectious disease or a tumor, by targeting an immune response against apathogen (such as a virus or fungus) or neoplasm. Therefore, bypurifying and generating a purified population of selectedantigen-specific T cells from a subject ex vivo and introducing atherapeutic amount of these cells, the immune response of the recipientsubject is enhanced. The administration of a therapeutically effectiveamount of a PD-1 antagonist also enhances the immune response of therecipient.

Methods of inducing an immune response to an antigen of interest in arecipient are provided herein. The recipient can be any subject ofinterest, including a subject with a chronic infection, such as a viralor fungal infection, or a subject with a tumor. These infections aredescribed above.

Infections in immune deficient people are a common problem in allograftstem cell recipients and in permanently immunosuppressed organtransplant recipients. The resulting T cell deficiency infections inthese subjects are usually from reactivation of viruses already presentin the recipient. For example, once acquired, most herpes group viruses(such as CMV, EBV, VZV, HSV) are dormant, and kept suppressed by Tcells. However, when patients are immunosuppressed by conditioningregimens, dormant viruses can be reactivated. For example, CMVreactivation, Epstein Barr virus (EBV) reactivation which causes a tumorin B cells (EBV lymphoproliferative disease), and BK virus reactivationwhich causes hemorrhagic cystitis, can occur followingimmunosuppression. In addition, HIV infection and congenital immunedeficiency are other examples of T cell immune deficiency. These viralinfections and reactivations can be an issue in immunosuppressedsubjects.

In several embodiments, an immune response against a tumor is providedto the recipient of a bone marrow transplant. Anti-tumor immunity can beprovided to a subject by administration of antigen-specific T cells thatrecognize a tumor-antigen. Such administration to a recipient willenhance the recipient's immune response to the tumor by providing Tcells that are targeted to, recognize, and immunoreact with a tumorantigen of interest.

In one example, the method includes isolating from the donor apopulation of donor cells including T cells (such as peripheral bloodmononuclear cells) and contacting a population of donor cells comprisingT cells with a population of antigen presenting cells (APCs) from thedonor that are presenting an antigen of interest, optionally in thepresence of PD-1, thereby producing a population of donor cellscomprising activated donor CD4+ and/or CD8+ T cells depleted foralloreactive T cells that recognize an antigen of interest. Atherapeutically effective amount of the population of donor activatedCD4+ and/or CD8+ cells into the recipient, thereby producing an immuneresponse to the antigen of interest in the recipient. Administration ofthe purified antigen-specific T cells can increase the ability of asubject to overcome pathological conditions, such as an infectiousdisease or a tumor, by targeting an immune response against a pathogen(such as a virus or fungus) or neoplasm. Thus, an immune response isproduced in the recipient against the antigen of interest.

In several embodiments the method also includes administering atherapeutically effective amount of a PD-1 antagonist to the subject.The administration of PD-1 antagonists is described in detail above.

Any antigenic peptide (such as an immunogenic fragment) from an antigenof interest can be used to generate a population of T cells specific forthat antigen of interest. Numerous such antigenic peptides are known inthe art, such as viral and tumor antigens (see, for example, Tables1-3). This disclosure is not limited to using specific antigen peptides.Particular examples of antigenic peptides from antigens of interest,include, but are not limited to, those antigens that are viral, fungal,and tumor antigens, such as those shown in Tables 1-3. Additionalantigenic peptides are known in the art (for example see Novellino etal., Cancer Immunol. Immunother. 54(3):187-207, 2005, and Chen et al.,Cytotherapy, 4:41-8, 2002, both herein incorporated by reference).

Although Tables 1 and 3 disclose particular fragments of full-lengthantigens of interest, one skilled in the art will recognize that otherfragments or the full-length protein can also be used in the methodsdisclosed herein. In one example, an antigen of interest is an“immunogenic fragment” of a full-length antigen sequence. An“immunogenic fragment” refers to a portion of a protein which, whenpresented by a cell in the context of a molecule of the MHC, can in aT-cell activation assay, activate a T-cell against a cell expressing theprotein. Typically, such fragments that bind to MHC class I moleculesare 8 to 12 contiguous amino acids of a full length antigen, althoughlonger fragments may of course also be used. In some examples, theimmunogenic fragment is one that can specifically bind to an MHCmolecule on the surface of an APC, without further processing of theepitope sequence. In particular examples, the immunogenic fragment is8-50 contiguous amino acids from a full-length antigen sequence, such as8-20 amino acids, 8-15 amino acids, 8-12 amino acids, 8-10 amino acids,or 8, 9, 10, 11, 12, 13, 14, 15 or 20 contiguous amino acids from afull-length antigen sequence. In some examples, APCs are incubated withthe immunogenic fragment under conditions sufficient for the immunogenicfragment to specifically bind to MHC molecules on the APC surface,without the need for intracellular processing.

In one example, an antigen includes a peptide from the antigen ofinterest with an amino acid sequence bearing a binding motif for an HLAmolecule of the subject. These motifs are well known in the art. Forexample, HLA-A2 is a common allele in the human population. The bindingmotif for this molecule includes peptides with 9 or 10 amino acidshaving leucine or methionine in the second position and valine orleucine in the last positions (see examples above). Peptides thatinclude these motifs can be prepared by any method known in the art(such as recombinantly, chemically, etc.). With knowledge of an aminoacid sequence of an antigen of interest, immunogenic fragment sequencespredicted to bind to an MHC can be determined using publicly availableprograms. For example, an HLA binding motif program on the Internet(Bioinformatics and Molecular Analysis Section-BIMAS) can be used topredict epitopes of any tumor-, viral-, or fungal-associated antigen,using routine methods. Antigens of interest (either full-length proteinsor an immunogenic fragment thereof) then can be produced and purifiedusing standard techniques. For example, epitope or full-length antigensof interest can be produced recombinantly or chemically synthesized bystandard methods. A substantially pure peptide preparation will yield asingle major band on a non-reducing polyacrylamide gel. In otherexamples, the antigen of interest includes a crude viral lysate.

In one example, the antigen of interest is a tumor associated antigenand the amino acid sequences bearing HLA binding motifs are those thatencode subdominant or cryptic epitopes. Those epitopes can be identifiedby a lower comparative binding affinity for the HLA molecule withrespect to other epitopes in the molecule or compared with othermolecules that bind to the HLA molecule.

Through the study of single amino acid substituted antigen analogs andthe sequencing of endogenously bound, naturally processed peptides,critical residues that correspond to motifs required for specificbinding to HLA antigen molecules have been identified (see, for example,Southwood et al., J. Immunol. 160:3363, 1998; Rammensee et al.,Immunogenetics 41:178, 1995; Rammensee et al., J. Curr. Opin. Immunol.10:478, 1998; Engelhard, Curr. Opin. Immunol. 6:13, 1994; Sette andGrey, Curr. Opin. Immunol. 4:79, 1992). Furthermore, x-raycrystallographic analysis of HLA-peptide complexes has revealed pocketswithin the peptide binding cleft of HLA molecules which accommodate, inan allele-specific mode, residues borne by peptide ligands; theseresidues in turn determine the HLA binding capacity of the peptides inwhich they are present. (See, for example, Madden, Annu. Rev. Immunol.13:587, 1995; Smith et al., Immunity 4:203, 1996; Fremont et al.,Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, Curr.Opin. Immunol. 9:75, 1997; Brown et al., Nature 364:33, 1993.)

The antigen of interest is selected based on the subject to be treated.For example, if the subject is in need of increased antiviral orantifungal immunity one or more target viral or fungal associatedantigens are selected. Exemplary antigens of interest from virusesinclude antigens from Epstein bar virus (EBV), hepatitis C virus (HCV)cytomegalovirus (CMV), herpes simplex virus (HSV), BK virus, JC virus,and human immunodeficiency virus (HIV) amongst others. Exemplaryantigens of interest from fungi include antigens from Candida albicans,Cryptococcus, Blastomyces, and Histoplasma, or other infectious agent.In another example, the subject is in need of increased anti-tumorimmunity. Exemplary antigens of interest from tumors include WT1, PSA,PRAME. Exemplary antigens of interest for infectious agents are listedin Table 1. In some examples, the antigen of interest includes both aviral antigen and a tumor antigen, both a fungal antigen and a tumorantigen, or a viral antigen, a fungal antigen, and a tumor antigen.

For the treatment of a subject with a tumor, the tumor antigen ofinterest is chosen based on the expression of the protein by therecipient's tumor. For example, if the recipient has a breast tumor, abreast tumor antigen is selected, and if the recipient has a prostatetumor, a prostate tumor antigen is selected, and so forth. Table 2 listsexemplary tumors and respective tumor associated antigens that can beused to generate purified antigen-specific T cells that can beadministered to a subject having that particular tumor. However, oneskilled in the art will recognize that the same and other tumors can betreated using additional tumor antigens.

In one example, antigen-specific T cells that recognize a tumor antigenare administered in a therapeutically effective amount to a subject whohas had, or will receive, a stem cell allograft or autograft, or who hasbeen vaccinated with the tumor antigen. For example, a therapeuticamount of antigen-specific T cells can be administered that recognizeone or more tumor-associated antigens, for example at least one of theantigens of interest listed in Tables 2-3.

In particular examples where the recipient has a tumor and has or willreceive a stem cell allograft, donor tumor antigen-specific T cells anda therapeutically effective amount of a PD-1 antagonist are administeredin a therapeutically effective amount after the stem cell allograft toprevent, decrease, or delay tumor recurrence, or to treat a malignantrelapse. The purified antigen-specific T cells can be introduced backinto the subject after debulking. In yet another example, the recipientis vaccinated with the tumor antigen of interest, purifiedantigen-specific T cells purified from the recipient and thenre-introduced into the recipient with a therapeutically effective amountof a PD-1 antagonist to increase the recipient's immune system againstthe tumor.

Administration of a therapeutic amount of tumor antigen-specific T cellsand a therapeutically effective amount of a PD-1 antagonist can be usedprophylactically to prevent recurrence of the tumor in the recipient, orto treat a relapse of the tumor. Such antigen-specific T cells can killcells containing the tumor-associated antigen or assist other immunecells.

In a specific example, a recipient has a tumor and has or will receive astem cell allograft to reconstitute immunity. Following bone marrowirradiation or administration of a cytotoxic drug that has ablated orotherwise compromised bone marrow function, at least two types of donorantigen-specific T cells are administered in a therapeutically effectiveamount; antigen-specific T cells that specifically recognize aviral-associated antigen (or a fungal-associated antigen) andantigen-specific T cells that specifically recognize a tumor-associatedantigen. In addition, a therapeutically effective amount of a PD-1antagonist is administered to the subject. Such administration can beused to induce an anti-tumor effect and an anti-viral effect (such as ananti-viral effect).

In order to produce a population of antigen-specific T cells foradministration to a subject of interest, a population of cells includingT cells can be contacted with antigen presenting cells (APCs), such asdendritic cells or T-APCs, to present the antigen of interest. In someembodiments, the responder T cells (such as lymphocytes or PBMCs) aretreated with an antagonist of PD-1 and are added to the APCs presentingone or more antigens of interest, and incubated under conditionssufficient to allow the interaction between the APCs presenting antigenand the T cells to produce antigen-specific T cells. The treatment ofthe responder T cells with the PD-1 antagonist can be simultaneouslywith the contact or the APCs. The treatment with the PD-1 antagonist canalso be immediately prior to the contact with the APCs.

Thus, methods are provided herein for producing an enriched populationof antigen-specific T cells. Generally, T-APCs present antigens to Tcells and induce an MHC-restricted response in a class I (CD8+ T cells)and class II (CD4+ T cells) restricted fashion. The typical T cellresponse is activation and proliferation. Thus, a population is producedthat includes T cells that specifically recognize an antigen ofinterest. Thus a therapeutically effective amount of this population ofcells can be administered to a subject to produce an immune response,such as a subject with a chronic infection or a tumor.

Generally, the APCs and the T cells are autologous. In specific,non-limiting examples, the APCs and the responder T cells are from thesame individual. However, the APCs and the responder T cells can besyngeneic. The APC can be used to present any antigen to a population ofautologous T cells. One of skill in the art will appreciate thatantigenic peptides that bind to MHC class I and II molecules can begenerated ex vivo (for example instead of being processed from afull-length protein in a cell), and allowed to interact with (such asbind) MHC I and II molecules on a cell surface. Generally, APCs presentantigen in the context of both MHC class I and II.

In one example, the antigen of interest incubated with the APCs is afusion protein that includes an amino acid sequence from the antigen ofinterest (such as 8-50 contiguous amino acids, for example 8-15 or 8-12contiguous amino acids from the antigen of interest). Thus, a series ofMHC binding epitopes can be included in a single antigenic polypeptide,or a single chain trimer can be utilized, wherein each trimer has an MHCclass I molecule, a b2 microglobulin, and an antigenic peptide ofinterest (see Nature 2005; vol. 436, page 578). In some examples, only asingle antigen is used, but in other embodiments, more than one antigenis used, such as at least 2 different antigens, at least 3 differentantigens, at least 4 different antigens, at least 5 different antigens,at least 10 different antigens, at least 15 different antigens, at least20 different antigens, or even at least 50 different antigens.

In yet other examples, an antigen of interest is a full-length antigenamino acid sequence (such as a full-length fungal antigen, tumorantigen, or viral antigen, for example a viral lysate or full-lengthcathepsin G). In additional examples, one or more antigens from anyinfectious agent can be utilized. In some examples, the full-lengthantigen of interest is expressed by the APC.

APCs can be produced using methods known to one of skill in the art (seeMelenhorst et al, Cytotherapy 7, supp. 1, 2005; Melenhorst et al., Blood106: 671a, 2005; Gagliardi et al., Int. Immunol. 7: 1741-52, 1995,herein incorporated by reference). In one example, to produce T-APCs,donor peripheral blood monocytes are activated using IL-2 and anantibody that specifically binds CD3 (such as OKT3) for about three ormore days, such as about one to two weeks, such as for about seven toten days.

It has been observed that in the presence of presenting antigen, T cellsthat recognize the antigen bind to antigen presenting cells (APCs)presenting an antigen of interest more strongly than do T cells that arenot specific for the antigen (and are thus not binding in anantigen-specific manner). In a particular example, antigen-specific Tcells are selected by exposing APCs to a target peptide antigen (such asa target viral or tumor associated antigen) against which desired Tcells are to be targeted in the presence of a PD-1 antagonist, such thatthe APC presents the antigen in association with a majorhistocompatability complex (MHC) class I and/or class II. For example,APCs can be exposed to a sufficient amount of a antigen of interest tosufficiently occupy MHC molecules on the surface of the APC (forexample, at least 1% of the MHC molecules are occupied, such at least5%, at least 7.5% or at least 10%) and stimulate preferential binding oftarget T cells in the presence of a PD-1 antagonist to the APCspresenting the antigen of interest (as compared to APCs that do notpresent the antigen of interest). A population of T cells, such aspopulation that has been primed for the antigen of interest, is thenincubated with the APCs, optionally in the presences of a PD-1antagonist, such as an antibody that specifically binds PD-1, topreferentially activate the cells, thereby producing a population ofcells enriched with the desired T cells that recognize the antigen ofinterest.

T cells, such as those present in a population of PBMCs or lymphocytes,can be incubated with one or more antigens of interest, optionally inthe presence of a PD-1 antagonist to generate a T cell population thatis primed for the one or more antigens of interest. T cells can beprimed using any method known in the art. In particular examples, PBMCsor lymphocytes are incubated in the presence of a purified targetpeptide antigen, optionally in the presence of a PD-1 antagonist. Insome examples, the antigen of interest is an antigen of an infectiousagent, or a tumor antigen, such as, but not limited to, one or more ofthe antigens of interest listed in the above tables. The antigen ofinterest can be in a purified form, such as a chemically synthesizedpeptide. In other examples, the antigen of interest is present in anon-purified form, such as in a crude lysate, for example a virallysate.

The amount of antigen used to prime T cells can be readily determinedusing methods known in the art. Generally, if the antigen is used in apurified form, about 1-10 μg/ml of peptide is used. When a viral lysateis used, about 0.1-100 μl of lysate, such as about 75 μl, can be used.When T-APCs are used, about 4-6 million T-APCs presenting the antigen ofinterest can be used for every 40-60 million T cells (or lymphocytes orPBMCs).

In a specific example, lymphocytes are primed in vitro by incubatingthem with soluble antigen or viral lysate for 5-7 days under conditionsthat permit priming of T cells. Viable T cells are recovered, forexample by Ficoll-Hypaque centrifugation, thereby generating primed Tcells. If desired, the viable primed T cells can be primed again one ormore times, for example by incubation with the antigen for another 5-7days under the same conditions as those used for the first priming, andviable T cells recovered.

In another example, lymphocytes are primed in vivo by inoculating asubject with the antigen, for example in the form of a vaccine. In thisexample, T cells obtained from the subject following immunization arealready primed. For example, lymphocytes or PBMC obtained from a subjectare then incubated with APCs in the presence of a PD-1 antagonist asdescribed herein, without the need for additional priming.

The method can further include generating the APCs that present theantigen of interest. For example, APCs can be incubated with asufficient amount of one or more different peptide antigens, underconditions sufficient for the target peptide(s) to be presented on thesurface of the APCs. This generates a population of APCs that presentthe antigen of interest on MHC molecules on the surface of the APC. Thedisclosed methods are not limited to particular methods of presentingthe antigen of interest on the surface of an APC.

Antigens can also be expressed by the APC either naturally or due to theinsertion of a gene containing the DNA sequence encoding the targetprotein (antigen). A nucleic acid encoding the antigen of interest canbe introduced into the T cells as messenger RNA, or using a vector, suchas a mammalian expression vector, or a viral vector (for example, aadenovirus, poxvirus, or retrovirus vectors). The polynucleotidesencoding an antigen of interest include a recombinant DNA which is anautonomously replicating plasmid or virus, or which is incorporated intothe genomic DNA of a eukaryote, or which exists as a separate moleculeindependent of other sequences. A nucleic acid encoding an antigen ofinterest can also be introduced using electroporation, lipofection, orcalcium phosphate-based transfection.

A number of viral vectors have been constructed, including polyoma,i.e., SV40 (Madzak et al., 1992, J. Gen. Virol., 73:15331536),adenovirus (Berkner, 1992, Cur. Top. Microbiol. Immunol., 158:39-6;Berliner et al., 1988, Bio Techniques, 6:616-629; Gorziglia et al.,1992, J. Virol., 66:4407-4412; Quantin et al., 1992, Proc. Nad. Acad.Sci. USA, 89:2581-2584; Rosenfeld et al., 1992, Cell, 68:143-155;Wilkinson et al., 1992, Nucl. Acids Res., 20:2233-2239;Stratford-Perricaudet et al., 1990, Hum. Gene Ther., 1:241-256),vaccinia virus (Mackett et al., 1992, Biotechnology, 24:495-499),adeno-associated virus (Muzyczka, 1992, Curr. Top. Microbiol. Immunol.,158:91-123; On et al., 1990, Gene, 89:279-282), herpes viruses includingHSV, CMV and EBV (Margolskee, 1992, Curr. Top. Microbiol. Immunol.,158:67-90; Johnson et al., 1992, J. Virol., 66:29522965; Fink et al.,1992, Hum. Gene Ther. 3:11-19; Breakfield et al., 1987, Mol. Neurobiol.,1:337-371; Fresse et al., 1990, Biochem. Pharmacol., 40:2189-2199),Sindbis viruses (H. Herweijer et al., 1995, Human Gene Therapy6:1161-1167; U.S. Pat. Nos. 5,091,309 and 5,2217,879), alphaviruses (S.Schlesinger, 1993, Trends Biotechnol. 11:18-22; I. Frolov et al., 1996,Proc. Natl. Acad. Sci. USA 93:11371-11377) and retroviruses of avian(Brandyopadhyay et al., 1984, Mol. Cell Biol., 4:749-754; Petropouploset al., 1992, J. Virol., 66:3391-3397), murine (Miller, 1992, Curr. Top.Microbiol. Immunol., 158:1-24; Miller et al., 1985, Mol. Cell Biol.,5:431-437; Sorge et al., 1984, Mol. Cell Biol., 4:1730-1737; Mann etal., 1985, J. Virol., 54:401-407), and human origin (Page et al., 1990,J. Virol., 64:5370-5276; Buchschalcher et al., 1992, J. Virol.,66:2731-2739). Baculovirus (Autographa californica multinuclearpolyhedrosis virus; AcMNPV) vectors are also known in the art, and maybe obtained from commercial sources (such as PharMingen, San Diego,Calif.; Protein Sciences Corp., Meriden, Conn.; Stratagene, La Jolla,Calif.).

In one embodiment, the polynucleotide encoding an antigen of interest isincluded in a viral vector for transfer into APC. Suitable vectorsinclude retrovirus vectors, orthopox vectors, avipox vectors, fowlpoxvectors, capripox vectors, suipox vectors, adenoviral vectors, herpesvirus vectors, alpha virus vectors, baculovirus vectors, Sindbis virusvectors, vaccinia virus vectors and poliovirus vectors. Specificexemplary vectors are poxvirus vectors such as vaccinia virus, fowlpoxvirus and a highly attenuated vaccinia virus (MVA), adenovirus,baculovirus and the like.

Pox viruses of use include orthopox, suipox, avipox, and capripox virus.Orthopox include vaccinia, ectromelia, and raccoon pox. One example ofan orthopox of use is vaccinia. Avipox includes fowlpox, canary pox andpigeon pox. Capripox include goatpox and sheeppox. In one example, thesuipox is swinepox. Examples of pox viral vectors for expression asdescribed for example, in U.S. Pat. No. 6,165,460, which is incorporatedherein by reference. Other viral vectors that can be used include otherDNA viruses such as herpes virus and adenoviruses, and RNA viruses suchas retroviruses and polio.

Suitable vectors are disclosed, for example, in U.S. Pat. No. 6,998,252,which is incorporated herein by reference. In one example, a recombinantpoxvirus, such as a recombinant vaccinia virus is synthetically modifiedby insertion of a chimeric gene containing vaccinia regulatory sequencesor DNA sequences functionally equivalent thereto flanking DNA sequenceswhich to nature are not contiguous with the flanking vaccinia regulatoryDNA sequences that encode an antigen of interest. The recombinant viruscontaining such a chimeric gene is effective at expressing the antigen.In one example, the vaccine viral vector comprises (A) a segmentcomprised of (i) a first DNA sequence encoding an antigen and (ii) apoxvirus promoter, wherein the poxvirus promoter is adjacent to andexerts transcriptional control over the DNA sequence encoding an antigenpolypeptide; and, flanking said segment, (B) DNA from a nonessentialregion of a poxvirus genome. The viral vector can encode a selectablemarker. In one example, the poxvirus includes, for example, a thymidinekinase gene (see U.S. Pat. No. 6,998,252, which is incorporated hereinby reference).

The population of APCs that present a sufficient density of theantigen(s) are incubated with T cells (such as lymphocytes or PBMCs),optionally in the presence of an effective amount of a PD-1 antagonist,under conditions sufficient to allow binding between the APCs presentingthe antigen and the T cells that can specifically immunoreact with theantigen (antigen-specific T cells). A sufficient number of APCsexpressing a sufficient density of antigen in combination with MHC tostimulate enhance binding of a target T cell to the APC are used. Inparticular examples, at least 20% of the APCs are presenting the desiredantigen on MHC molecules on the APC surface, such as at least 30% of theAPCs, at least 40% of the APCs, at least 50% of the APCs, or at least60% of the APCs. The optimal amount of T cells added can vary dependingon the amount of APCs used. In some examples, a T cell:APC ratio of atleast 6:1 is used, such as at least 8:1, at least 10:1, at least 12:1,at least 15:1, at least 16:1, at least 20:1, or even at least 50:1.

To increase the number of antigen-specific T cells, proliferation of thecells can be stimulated, for example by incubation in the presence of acytokine, such as IL-2, IL-7, IL-12 and IL-15. The amount of cytokineadded is sufficient to stimulate production and proliferation of Tcells, and can be determined using routine methods. In some examples,the amount of IL-2, IL-7, IL-12, or IL-15 added is about 0.1-100 IU/mL,such as at least 1 IU/mL, at least 10 IU/mL, or at least 20 IU/mL.

After a sufficient amount of binding of the antigen specific T cells tothe APCs, T cells that specifically recognize the antigen of interestare produced. This generates a population of enriched (such as purified)antigen-specific T cells that are specific for the antigen of interest.In some examples, the resulting population of T cells that are specificfor the antigen of interest is at least 30% pure, such as at least 40%pure, or even at least 50% pure. The purity of the population of antigenspecific T cells can be assessed using methods known to one of skill inthe art.

In one example, during stimulation of proliferation of antigen-specificT cells, the cells can be counted to determine the cell number. When thedesired number of cells is achieved, purity is determined. Purity can bedetermined, for example, using markers present on the surface ofantigen-specific T cells concomitant with the assessment of cytokineproduction upon antigen recognition, such as interferon (IFN)?, tumornecrosis factor (TNF)α, interleukin (IL)-2, IL-10, transforming growthfactor (TGF)β1, or IL-4. Generally, antigen-specific T cells arepositive for the CD3 marker, along with the CD4 or CD8 marker, and IFN-γ(which is specific for activated T cells). For example, fluorescenceactivated cell sorting (FACS) can be used to identify (and sort ifdesired) populations of cells that are positive for CD3, CD4 or CD8, andIFN-γ by using differently colored anti-CD3, anti-CD4, anti-CD8 andanti-IFN-γ. Briefly, stimulated T antigen-specific cells are incubatedin the presence of anti-CD3, anti-CD4, anti-CD8 and anti-IFN-γ (eachhaving a different fluorophore attached), for a time sufficient for theantibody to bind to the cells. After removing unbound antibody, cellsare analyzed by FACS using routine methods. Antigen-specific T cells arethose that are INF-γ positive and CD8 positive or CD4 positive. Inspecific examples, the resulting population of antigenic T cells is atleast 30% pure relative to the total population of CD4+ or CD8+ positivecells, such as at least 40% pure, at least 50% pure, at least 60% pure,or even at least 70% pure relative to the total population of CD4positive or CD8 positive cells.

In another example, the method further includes determining thecytotoxicity of the antigen-specific T cells. Methods for determiningcytotoxicity are known in the art, for example a ⁵¹Cr-release assay (forexample see Walker et al. Nature 328:345-8, 1987; Qin et al. ActaPharmacol. Sin. 23(6):534-8, 2002; all herein incorporated byreference).

The antigen-specific T cells can be subjected to one or more rounds ofselection to increase the purity of the antigen-specific T cells. Forexample, the purified antigen-specific T cells generated above are againincubated with APCs presenting the antigen of interest in the presenceof a PD-1 antagonist under conditions sufficient to allow bindingbetween the APCs and the purified antigen-specific T cells. Theresulting antigen-specific T cells can be stimulated to proliferate, forexample with IL-2. Generally, the resulting antigen-specific T cellsthat specifically immunoreact with the antigen of interest are more pureafter successive stimulations with APCs than with only one round ofselection. In one example, the population of purified antigen-specific Tcells produced is at least 90% pure relative to all CD3+ cells present,such as at least 95% pure or at least 98% pure. In a particular example,the population of purified antigen-specific T cells produced is at least95% pure relative to all CD4+ cells present, such as at least 98% pure.In another example, the population of purified antigen-specific T cellsproduced is at least 90% pure relative to all CD3+ cells present, suchas at least 93% pure.

The present disclosure also provides therapeutic compositions thatinclude the enriched (such as purified) antigen-specific T cells and aPD-1 antagonist. In particular examples, the resulting enrichedpopulation of antigen-specific T cells (specific for the antigen ofinterest) are placed in a therapeutic dose form for administration to asubject in need of them. The PD-1 antagonist is also present in atherapeutic dose form for administration to a subject in need oftreatment.

In one example, the population of purified antigen-specific T cellsproduced is at least 30% pure relative to all CD3+ cells present, suchas at least 40% pure, at least 50% pure, at least 80% pure, or even atleast 90% pure. In a particular example, the population of purifiedantigen-specific T cells produced is at least 30% pure relative to allCD3+ cells present, such as at least 40% pure, at least 50% pure, atleast 80% pure, at least 90% pure, at least 95% pure, or even at least98% pure. In another example, the population of purifiedantigen-specific T cells produced is at least 50% pure relative to allCD3+ cells present, such as at least 60% pure, at least 75% pure, atleast 80% pure, at least 90% pure, or even at least 93% pure. Expandedand selected antigen-specific T cells can be tested for mycoplasma,sterility, endotoxin and quality controlled for function and purityprior cryopreservation or prior to infusion into the recipient.

A therapeutically effective amount of antigen-specific T cells isadministered to the subject. Specific, non-limiting examples of atherapeutically effective amount of purified antigen-specific T cellsinclude purified antigen-specific T cells administered at a dose ofabout 1×10⁵ cells per kilogram of subject to about 1×10⁹ cellsperkilogram of subject, such as from about 1×10⁶ cells per kilogram toabout 1×10⁸ cells per kilogram, such as from about 5×10⁶ cells perkilogram to about 75×10⁶ cells per kilogram, such as at about 25×10⁶cells per kilogram, or at about 50×10⁶ cells per kilogram.

Purified antigen-specific T cells can be administered in single ormultiple doses as determined by a clinician. For example, the cells canbe administered at intervals of approximately two weeks depending on theresponse desired and the response obtained. In some examples, once thedesired response is obtained, no further antigen-specific T cells areadministered. However, if the recipient displays one or more symptomsassociated with infection or the presence or growth of a tumor, atherapeutically effective amount of antigen-specific T cells can beadministered at that time. The administration can be local or systemic.

The purified antigen-specific T cells disclosed herein can beadministered with a pharmaceutically acceptable carrier, such as saline.The PD-1 antagonist can also be formulated in a pharmaceuticallyacceptable carrier, as described above. In some examples, othertherapeutic agents are administered with the antigen-specific T cellsand PD-1 antagonist. Other therapeutic agents can be administeredbefore, during, or after administration of the antigen-specific T cells,depending on the desired effect. Exemplary therapeutic agents include,but are not limited to, anti-microbial agents, immune stimulants such asinterferon-alpha, chemotherapeutic agents or peptide vaccines of thesame antigen used to stimulate T cells in vitro. In a particularexample, compositions containing purified antigen-specific T cells alsoinclude one or more therapeutic agents.

Methods of Treatment and Evaluation

It is disclosed herein that administration of a therapeuticallyeffective amount of PD-1 antagonist affect B cells, such as byincreasing the proliferation of memory B cells. Methods of treatment areprovided herein that include the administration of a PD-1 antagonist toa subject, as described above. These methods include measuring B cells,such as but not limited to measuring the proliferation of memory B cellsin the subject. In some examples, the methods include measuring naïve Bcells in a sample from the subject. In some embodiments, the methodsinclude measuring CD28 T cells and/or measuring neutralizing antibodiesto an antigen of interest. Thus, the methods can include measuring oneor more of memory B cell proliferation, naïve B cells, CD28 T cells, andneutralizing antibodies.

Methods are also provided herein to treat, and measure the efficacy of aPD-1 antagonist, in a variety of infections and cancers. The presentdisclosure encompasses methods to determine if treatment methods areeffective in any subject of interest. In these methods, a subject ofinterest is selected, such as a subject with a persistent infection orcancer. This subject is administered a therapeutically effective amountof a PD-1 antagonist. In some examples, memory B cell proliferation isassessed to determine if the treatment method was effective, and/or todetermine if the dose of the PD-1 antagonist should be altered. Inadditional examples, the methods include measuring naïve B cells. Infurther examples, the methods include measuring CD28 T cells and/ormeasuring neutralizing antibodies to an antigen of interest. Thus, themethods can include measuring one or more of memory B cellproliferation, naïve B cells, CD28 T cells, and neutralizing antibodies.

The subject can be any mammal such as human, a primate, mouse, rat, dog,cat, cow, horse, and pig. In several examples, the subject is a primate,such as a human. In additional examples, the subject is a murinesubject, such as a mouse. In several embodiments, the subject is at riskof developing infection, as discussed above. A subject at risk ofdeveloping infection is a subject that does not yet have the infection,but can be infected by the infectious agent of interest. In additionalexamples, a subject is selected for treatment that has an infection,such as a persistent infection. In other embodiments, the subject is atrisk of developing cancer or has cancer, as discussed above. Thesesubjects can be identified by standard methods suitable by one of skillin the art, such as a physician. The disclosed methods include selectinga subject of interest, and administering a PD-1 antagonist, as describedabove. Memory B cell proliferation is then assessed. In some examples,the number of naïve B cells is also assessed.

In some embodiments, the subject has a persistent infection with abacteria virus, fungus, or parasite, as described above. Atherapeutically effective amount of a PD-1 antagonist is administered totreat the subject. Memory B cell proliferation is then assessed todetermine if the treatment method was effective, and/or to determine ifthe dose of the PD-1 antagonist should be altered. Generally, persistentinfections, in contrast to acute infections are not effectively clearedby the induction of a host immune response. The infectious agent and theimmune response reach equilibrium such that the infected subject remainsinfectious over a long period of time without necessarily expressingsymptoms. Persistent infections include for example, latent, chronic andslow infections. Persistent infection occurs with viruses such as humanT-Cell leukemia viruses, XMRV, polyoma JC virus, Epstein-Barr virus,cytomegalovirus, herpesviruses, varicella-zoster virus, measles,papovaviruses, prions, hepatitis viruses, adenoviruses, parvoviruses andpapillomaviruses. Additional persistent infections are described above.These methods can include measuring naïve B cells, CD28 T cells and/orneutralizing antibodies.

In further embodiments, the subject has a tumor. A therapeuticallyeffective amount of a PD-1 antagonist is administered to the subject totreat the tumor, as described above. Memory B cell proliferation is thenassessed to determine if the treatment method was effective, and/or todetermine if the dose of the PD-1 antagonist should be altered. Inseveral examples, a therapeutically effective amount of a tumor antigen,or a nucleotide encoding the tumor antigen, is also administered to thesubject. The PD-1 antagonist and the tumor antigen, or nucleotideencoding the tumor antigen, can be administered simultaneously orsequentially. These methods can include measuring naïve B cells, CD28 Tcells and/or neutralizing antibodies.

In additional embodiments, the subject is administered a therapeuticallyeffective amount of cytoxic T cells specific for an antigen of interest,such as a viral antigen or a tumor antigen, and a therapeuticallyeffective amount of a PD-1 antagonist. Administration of the purifiedantigen-specific T cells and PD-1, as disclosed herein, will increasethe ability of a subject to overcome pathological conditions, such as aninfectious disease or a tumor, by targeting an immune response against apathogen (such as a virus or fungus) or neoplasm. Therefore, bypurifying and generating a purified population of selectedantigen-specific T cells from a subject ex vivo and introducing atherapeutic amount of these cells, the immune response of the recipientsubject is enhanced. The administration of a therapeutically effectiveamount of a PD-1 antagonist also enhances the immune response of therecipient. Memory B cell proliferation is then assessed to determine ifthe treatment method was effective, and/or to determine if the dose ofthe PD-1 antagonist and/or cytotoxic T cells should be altered. Thesemethods can include measuring naïve B cells, CD28 expressing (CD28+) Tcells and/or neutralizing antibodies.

Thus, the methods disclosed herein for determining if a PD-1 antagonistis effective, or for determining the dose of a PD-1 antagonist iseffective, can be used in combination with any of the therapeuticmethods (and in any of the subjects) described above.

In some embodiments, memory B cells are measured. An increase in theproliferation of memory B cells from the a biological sample as comparedto a control indicates that the dose of the PD-1 antagonist is of usetreating the subject, and wherein an absence of a significant alterationin the proliferation of memory B cells as compared to the controlindicates that the dose of the PD-1 antagonist is not of use to treatthe subject.

In additional embodiments, the methods include detecting neutralizingantibodies in a biological sample from the subject, wherein an increasein neutralizing antibodies as compared to a control indicates that thedose of the PD-1 antagonist is of use treating the subject, and whereinan absence of a significant alteration in neutralizing antibodies ascompared to the control indicates that the dose of the PD-1 antagonistis not of use to treat the subject. In further embodiments, the methodsinclude detecting CD28 expressing (CD28+) T cells in a biological samplefrom the subject, wherein an increase in CD28+ T cells as compared to acontrol indicates that the that a dose of the PD-1 antagonist is of usetreating the subject, and wherein an absence of a significant alterationin CD28+ T cells as compared to the control indicates that the dose ofthe PD-1 antagonist is not of use to treat the subject. Thesemeasurements can be performed in addition to measuring memory B cells,but can also be performed in the absence of measuring memory B cells.

Additional methods are disclosed herein to determine whether aparticular PD-1 antagonist, or a particular dose of a PD-1 antagonist,is effective for treating a subject. These methods include measuring theproliferation of memory B cells, such as in a sample from the subject.These methods can also include measuring naïve B cells in a sample fromthe subject. For example, the expression of CD27, CD20 and CD21 can beevaluated (see below). In some examples, the measurement of memory Bcells and/or naïve B cells occurs after a sufficient period of time forthe PD-1 antagonist to decrease PD-1 activity in the subject.

The methods can also be used to evaluate the dose of a PD-1 antagonistthat is therapeutically effective for a subject. For example, themethods disclosed herein can be used to determine if the doseadministered to a subject of interest can be lowered and still beeffective. The methods disclosed herein also can be used to determine ifthe dose administered to a subject is too low, and thus must beincreased to be therapeutically effective.

In some embodiments, a first dose of a PD-1 antagonist is administeredto the subject. An increase in proliferating memory B cells, as comparedto a control, indicates that this dose is effective. In some cases, itcan be advantageous to decrease the amount of an agent administered to asubject, such as to decrease side effects. Thus, if the first doseincreases the proliferation of memory B cells, a second lower dose ofthe PD-1 antagonist can be administered to the subject, and a secondsample including B cells can be obtained. An increase in theproliferation of memory B cells from the second sample as compared to acontrol indicates that the second dose of the PD-1 antagonist is of usetreating the subject, and thus determines that the lower dose will betherapeutically effective for treating the subject. An absence of asignificant alteration in the proliferation of memory B cells in thesecond sample as compared to the control indicates that the second doseof the PD-1 antagonist is not therapeutically effective to treat thesubject. The method can be repeated to determine the lowesttherapeutically effective dose for a subject of interest.

In additional embodiments, a first dose of a PD-1 antagonist isadministered to the subject. A lack of an increase in the proliferationof memory B cells, as compared to a control, indicates that this dose isnot therapeutically effective for treating the subject. If the firstdose did not increase the proliferation of memory B cells, a secondhigher dose can be administered to the subject, and a second sampleincluding B cells can be obtained. An increase in the proliferation ofmemory B cells from the second sample as compared to a control indicatesthat the second higher dose of the PD-1 antagonist is of use treatingthe subject, and thus determines that the higher dose will betherapeutically effective for treating the subject. An absence of asignificant alteration in the proliferation of memory B cells in thesecond sample as compared to the control indicates that the second doseof the PD-1 antagonist is not therapeutically effective to treat thesubject, and thus that a third higher dose is required. Thus, the methodcan be repeated to determine a therapeutically effective dose for asubject of interest.

The methods disclosed can also be used to determine if a particular PD-1antagonist is therapeutically effective for treating a subject, and thusshould be continued, or if the particular PD-1 antagonist is noteffective for treating a subject, and thus that a different PD-1antagonist should be utilized to treat the subject. These methodsinclude administering a particular PD-1 antagonist to the subject, andassessing the proliferation of memory B cells in the sample from thesubject. An increase in the proliferation of memory B cells in thesample as compared to a control indicates that the particular PD-1antagonist is of use treating the subject. An absence of a significantalteration in the proliferation of memory B cells in the sample ascompared to the control indicates that the particular PD-1 antagonist isnot therapeutically effective to treat the subject, and that a differentPD-1 antagonist or other therapeutic agent should be administered to thesubject.

Thus, the efficacy of a specific PD-1 antagonist can be monitored, orthe effective dose of a PD-1 antagonist can be determined, using themethods disclosed herein. Generally, an increase in proliferation ofmemory B cells from a sample from a subject administered a PD-1antagonist, as compared to a control, indicates that the PD-1 antagonistis therapeutically effective for a subject, and/or indicates that thedose is sufficient for treating the subject.

Generally, measuring the proliferation of memory B cells includesobtaining a sample that includes B cells from a subject, and determiningthe presence or number of proliferating memory B cells in the sample. Insome examples, the sample is a biopsy sample, a blood sample, or asample of peripheral blood mononuclear cells. The sample can bepurified, for example to separate B cells, such as memory B cells and/ornaïve B cells. In some embodiments, the methods include measuring thequantity of proliferating memory B cells and/or the quantity of naïve Bcells in a sample from a subject administered a PD-1 antagonist ofinterest. In some examples, the quantity of proliferating memory B cellsand/or the quantity of naïve B cells is compared to a control. Withregard to proliferating memory B cells, the control can be a previouslydetermined standard value, or the quantity of proliferating memory Bcells from a subject not administered the PD-1 antagonist, or thequantity of proliferating memory B cells from a subject administered acontrol substance, such as vehicle alone. Similarly, with regard tonaïve B cells, the control can be a previously determined standardvalue, or the quantity of naïve B cells from a subject not administeredthe PD-1 antagonist, or the quantity of naïve B cells from a subjectadministered a control substance, such as vehicle alone, or the quantityof naïve B cells in a subject, respectively.

In some examples, memory B cells are identified that express CD27, suchas those cells that express CD20 and CD27, but do not express CD21(CD20⁺CD27⁺CD21⁻) compared to naïve B cells, which express CD20 andCD21, but do not express CD27 (CD20⁺CD27⁻CD21⁺). Memory B cells andnaïve B cells can be isolated and/or detected using antibodies thatspecifically bind CD20, CD21 and CD27. In some embodiments, memory Bcells express CD27 (CD27⁺). In some examples, memory B cells areidentified as CD27⁺CD21⁻B cells, such as CD20^(hi)/CD21⁻/CD27⁺(activatedmemory).

Methods for isolating and detecting B cells are known in the art, andexemplary protocols are provided herein. Methods also are known in theart to measure the proliferation of memory B cells and/or to measurenaïve B cells. These methods generally involve the use of molecularand/or biochemical techniques and not simple visual observation. In someexamples, fluorescence activated cell sorting

(FACS) is utilized. FACS can be used to sort (isolate) cells such asimmature B cells or differentiated plasma cells or memory cells, bycontacting the cells with an appropriately labeled antibody. In oneembodiment, several antibodies (such as antibodies that bind CD27, CD20,CD21, CD45R, CD40, CD19, and/or IgM) and FACS sorting can be used toproduce substantially purified populations of immature

B cells, plasma cells and or memory B cells.

Methods are also known for measuring CD28 T cells in a sample from asubject. These methods generally involve the use of molecular and/orbiochemical techniques and not simple visual observation. In someexamples, fluorescence activated cell sorting (FACS) is utilized. FACScan be used to sort (isolate) cells such as immature B cells ordifferentiated plasma cells or memory cells, by contacting the cellswith an appropriately labeled antibody. In one embodiment, severalantibodies (such as antibodies that bind CD3, CD4, CD8 and CD28) andFACS sorting can be used to produce substantially purified populationsof CD28+ T cells. Methods for the detection of neutralizing antibodiesare also known in the art. These assays include obtaining a biologicalsample and detecting the binding of antibodies to an antigen ofinterest, as well as specific neutralization assays, such as for avirus, for example HIV.

FACS employs a plurality of color channels, low angle and obtuselight-scattering detection channels, and impedance channels, among othermore sophisticated levels of detection, to separate or sort cells. AnyFACS technique can be employed as long as it is not detrimental to theviability of the desired cells. (For exemplary methods of FACS see U.S.Pat. No. 5,061,620).

However, other techniques of differing efficacy can be employed topurify and isolate desired populations of cells. The separationtechniques employed should maximize the retention of viability of thefraction of the cells to be collected. The particular technique employedwill, of course, depend upon the efficiency of separation, cytotoxicityof the method, the ease and speed of separation, and what equipmentand/or technical skill is required.

Separation procedures include magnetic separation, using antibody-coatedmagnetic beads, affinity chromatography, cytotoxic agents, either joinedto a monoclonal antibody or used in conjunction with complement, and“panning,” which utilizes a monoclonal antibody attached to a solidmatrix, or another convenient technique. Antibodies attached to magneticbeads and other solid matrices, such as agarose beads, polystyrenebeads, hollow fiber membranes and plastic petri dishes, allow for directseparation. Cells that are bound by the antibody can be removed from thecell suspension by simply physically separating the solid support fromthe cell suspension. The exact conditions and duration of incubation ofthe cells with the solid phase-linked antibodies will depend uponseveral factors specific to the system employed. The selection ofappropriate conditions, however, is well within the skill in the art.

The unbound cells then can be eluted or washed away with physiologicbuffer after sufficient time has been allowed for the cells expressing amarker of interest (e.g., CD45R or CD27) to bind to the solid-phaselinked antibodies. The bound cells are then separated from the solidphase by any appropriate method, depending mainly upon the nature of thesolid phase and the antibody employed.

Antibodies can be conjugated to biotin, which then can be removed withavidin or streptavidin bound to a support, or fluorochromes, which canbe used with a fluorescence activated cell sorter (FACS), to enable cellseparation.

For example, cells expressing CD45R and/or CD27 are initially separatedfrom other cells by the cell-surface expression of CD45R or CD27. In onespecific, non-limiting example, CD45R⁺ or CD27+ cells are positivelyselected by magnetic bead separation, wherein magnetic beads are coatedwith CD45 or CD27 reactive monoclonal antibody. The CD45R⁺ or CD27⁺cells are then removed from the magnetic beads.

Release of the CD45R⁺ cells or CD27⁺ cells from the magnetic beads caneffected by culture release or other methods. Purity of the isolatedCD45R⁺ cells or CD27⁺ cells is then checked, such as with a FACSCAN®flow cytometer (Becton Dickinson, San Jose, Calif.), if so desired. Inone embodiment, further purification steps are performed, such as FACSsorting the population of cells released from the magnetic beads. In oneexample, this sorting can be performed to detect expression of MHC classII, IgM, CD19, and CD40, in order to detect or isolate immature B cells.In another example, mature B cells can be isolated and/or detected onthe basis of expression of IgD and/or CD21, in addition to MHC class II,IgM, CD14, and CD40.

Methods for analyzing B cell proliferation, such as the assessment ofthe proliferation of memory B cells are known in the art. For example,membrane dye dilution approaches can be utilized which include ex vivochemical labeling of cells of interest with fluorescent dyes. Labelingwith tritiated nucleoside analogues (commonly ³H-thymidinedeoxyribonucleoside, ³H-TdR) or bromodeoxyuridine (BrdU) can beutilized. FACS analysis is available for the measurement of BrdUincorporation. Surrogate markers of proliferation such as DNA contentand cell cycle-associated proteins, can also be used.

In one example, measurement of Ki67 or PCNA can be utilized. Ki67antigen is the prototypic cell cycle related nuclear protein that isexpressed by proliferating cells in all phases of the active cell cycle(G1, S, G2 and M phase). It is absent in resting (G0) cells. Ki67antibodies are useful in establishing proliferation. Ki67 antibodies canbe used to quantify proliferating cells among and resting cells (Ki67index). Ki67 is routinely used as a marker of cell cycling andproliferation; antibodies to Ki67 are commercially available, such asfrom ABCAM®, and methods are available to use these antibodies inimmunohistochemical and FACS analyses.

Other methods can be used to detect those cells that are in the activecell cycle at the time of sampling. Proliferation of lymphocytes, suchas memory B cells, can also be measured by using methods that utilizestable isotopes to label DNA in biological samples including cells. DNAis uniformly and highly labeled via the de novo synthesis pathway. Thestable isotope labels used, e.g. ²H-glucose or heavy water (²H₂O or H₂¹⁸O), are non-toxic to animals and humans, and generally regarded assafe by the US Food and Drug Administration (FDA) (see U.S. PatentApplication Publication No. 2009/0155179). The measurement of stableisotope label incorporation into lymphocyte DNA comprises the followingsteps: (i) extraction of DNA or its release from chromatin withoutfurther isolation, hydrolysis of DNA to deoxyribonucleotides, (ii)selective release of deoxyribose from purine deoxyribonucleotides, (iii)derivatization of purine deoxyribose to a volatile derivative (e.g.,pentane tetraacetate, pentafluorobenzyl tetraacetyl derivative, oranother suitable derivative) suitable for analysis by gaschromatography/mass spectrometry (GC/MS), (iv) GC/MS analysis of saidderivative, (v) analysis of the pattern of mass isotopomer abundance ofsaid derivative, and (vi) calculation from said pattern of an excessenrichment value that is a measure of stable isotope incorporation.Specific embodiments of each of these methods have been taught (see U.S.Pat. No. 5,910,40).

In Vitro Assay

Methods are disclosed herein for selecting a PD-1 antagonist. Thesemethods include determining if an agent of interest is a PD-1antagonist. Thus, the methods include screening a nubmer of agent todetermine if they function as PD-1 antagoinists. This can be a libraryof compounds, small molecules or antibodies, and the assay can beconducted in a high-throughput format.

The methods also include determining if a specific PD-1 antagonist willbe of use to treat a specific individual of interest. Thus, thesedisclosed methods can be used for “personalized medicine” wherein thepopulation of cells is from a specific individual of interest, and anumber of potential PD-1 antagonist are tested to determine the PD-1antagonist most suited for treating that paritcular individual.

The methods include contacting an isolated population of cellscomprising memory B cells with an agent in vitro. In some embodiments,the population of cells is peripheral blood mononuclear cells orpurified memory B cells, such as activated or resting memory B cells. Inone example, the population of cells is a memory B cell line.

The methods can include detecting the proliferation of memory B cellsand/or detecting the differentiation of memory B cells into antibodysecreting cells. In several embodiments, the methods include assays todetect IgM, IgG and antibody-producing B cells. The assay can be anELISPOT assay. ELISPOT assays employ a technique very similar to thesandwich enzyme-linked immunosorbent assay (ELISA) technique. Either amonoclonal or polyclonal capture antibody is coated aseptically onto aPVDF (polyvinylidene fluoride)-backed microplate. These antibodies arechosen for their specificity for the analyte in question. The plate isblocked, usually with a serum protein that is non-reactive with any ofthe antibodies in the assay. After this, cells of interest are platedout at varying densities, along with antigen or mitogen, and then placedin a humidified 37° C. CO₂ incubator for a specified period of time.

Cytokine (or other cell product of interest, such as IgM or IgGantibodies) secreted by activated cells is captured locally by thecoated antibody on the high surface area PVDF membrane. After washingthe wells to remove cells, debris, and media components, a biotinylatedpolyclonal antibody specific for the chosen analyte is added to thewells. This antibody is reactive with a distinct epitope of the targetand thus is employed to detect the captured producted of interest.Following a wash to remove any unbound biotinylated antibody, thedetected product is then visualized, such as using using anavidin-enzyme, and a precipitating substrate for the enzyme. The coloredend product (a spot, usually colored) typically represents an individualproduct-producing cell. The spots can be counted manually (such as witha dissecting microscope) or using an automated reader to capture themicrowell images and to analyze spot number and size.

The proliferation of memory B cells can also be assessed. Suitableassays are disclosed herein (see above). Methods for analyzing B cellproliferation, such as the assessment of the proliferation of memory Bcells are known in the art. For example, membrane dye dilutionapproaches (commonly ³H-thymidine deoxyribonucleoside, ³H-TdR) orbromodeoxyuridine (BrdU) can be utilized. FACS analysis is available forthe measurement of BrdU incorporation. Surrogate markers ofproliferation such as DNA content and cell cycle-associated proteins,can also be used. In one example, measurement of Ki67 or PCNA can beutilized. Other methods can be used to detect those cells that are inthe active cell cycle at the time of sampling. Proliferation oflymphocytes, such as memory B cells, can also be measured by usingmethods that utilize stable isotopes to label DNA in biological samplesincluding cells. A exemplary, non-limited protocol for one assay of useis provided in the Examples section below.

Genterally, an increase of the proliferation of memory B cells and/or anincrease in the differentiation of memory B cells into antibodysecreting cells and/or in increase in antibody production indcates thatthe agent is a PD-1 antagonist. The increase of the proliferation ofmemory B cells and/or an increase in the differentiation of memory Bcells into antibody secreting cells and/or in increase in antibodyproduction can indicate that a specific PD-1 antagonist will be of usein treating a subject.

The disclosure is illustrated by the following non-limiting Examples.

EXAMPLES Example 1 Inhibition of the PD-1 Pathway inChronically-Infected Mice Using Anti-PD-L1 Antibodies

Mice infected with various strains of the lymphocytic choriomeningitisvirus (LCMV) were used to study the effect of chronic viral infection onCD8+ T cell function. The LCMV Armstrong strain causes an acuteinfection that is cleared within 8 days, leaving behind a long-livedpopulation of highly functional, resting memory CD8+ T cells. The LCMVCl-13 strain, in contrast, establishes a persistent infection in thehost, characterized by a viremia that lasts up to 3 months. The virusremains in some tissues indefinitely and antigen specific CD8+ T cellsbecome functionally impaired. DbNP396-404 CD8+ T cells are physicallydeleted, while DbGP33-41 and DbGP276-286 CD8+ T cells persist but losethe ability to proliferate or secrete anti-viral cytokines, such asIFN-γ and TNF-α.

C57BL/6 mice were purchased from the National Cancer Institute(Frederick, Md.). Mice were infected intravenously (i.v.) with 2×10⁶ pfuof LCMV-Cl-13. CD4 depletions were performed by injecting 500 μg ofGK1.5 in PBS the day of infection and the day following the infection.LCMV immune mice are generated by infecting mice i.p. with 2×105 pfuLCMV Armstrong.

Gene array analysis was performed on FACS-purified naïve DbGP33-41specific P14 transgenic CD8+ T cells, DbGP33-41 specific memory CD8+ Tcells derived from LCMV Armstrong immune mice, and DbGP33-41 specific orDbGP276-286 specific CD8+ T cells derived from CD4+ depleted LCMV C1-13infected mice. RNA isolation and gene array analysis were performed asdescribed in Kaech et al., (Cell 111:837-51, 2002). PD-1 mRNA was highlyexpressed in exhausted CD8+ T cells relative to memory CD8+ T cells(FIG. 1A). Furthermore, PD-1 was expressed on the surface of CD8+ Tcells in LCMV C1-13 infected mice, but was not present on the surface ofCD8+ T cells after clearance of LCMV Armstrong (FIG. 1B). Chronicallyinfected mice also expressed higher levels of one of the ligands ofPD-1, PD-L1, on most lymphocytes and APC compared to uninfected mice.Thus, viral antigen persistence and CD8+ T cell exhaustion areconcomitant with an induction in PD-1 expression.

To test the hypothesis that blocking the PD-1/PD-L1 pathway may restoreT cell function and enhance viral control during chronic LCMV infection,the PD-1/PD-L1 co-inhibitory pathway was disrupted during chronic LCMVinfection using αPD-L1 blocking antibodies. A blocking monoclonalantibody against PD-L1 was administered intraperitoneally (i.p.) everythird day to mice infected with LCMV Cl-13 (200 μg of rat anti-mousePD-L1 IgG2b monoclonal antibodies (clone 10F.5C5 or 10F.9G2)) from day23 to day 37 post-infection. At day 37, there was approximately 2.5 foldmore DbNP396-404 specific CD8+ T cells and 3 fold more DbGP33-41specific CD8+ T cells in treated mice relative to the untreated controls(FIG. 2A). The induction in proliferation was specific to CD8+ T cellssince the number of CD4+ T cells in the spleen were approximately thesame in both treated mice and untreated mice (6×104 IAbGP61-80 of CD4+ Tcells per spleen).

In addition to an increase in CD8+ T cell proliferation, the inhibitionof PD-1 signaling also resulted in an increased production of anti-viralcytokines in virus-specific CD8+ T cells. The production of IFN-γ andTNF-α by CD8+ T cells to eight different CTL epitopes was determined.The combined response was 2.3 fold higher in treated mice as compared tountreated mice (FIGS. 2B and 2C). A 2-fold increase in the frequency ofTNF-α producing cells was also observed following treatment (FIG. 2D).Viral clearance was also accelerated as the virus was cleared from theserum, spleen, and liver of treated mice. Reduced viral titers wereobserved in the lung and kidney (˜10 fold) by day 37 post-infection (14days following initiation of treatment) in treated mice. Untreated mice,however, displayed significant levels of virus in all these tissues(FIG. 2E). Viral titers in serum and tissue homogenates were determinedusing Vero cells, as described in Ahmed et al. (J. Virol. 51:34-41,1984). The results showing that a PD-1 antagonist increases CD8+ T cellproliferation and viral clearance therefore indicate that the inhibitionof PD-1 signaling restores CD8+ T cell function. Furthermore, inhibitionof PD-1 signaling also enhanced B cell responses as the number of LCMVspecific antibody secreting cells in the spleen was also increased(>10-fold) following treatment.

CD4+ T cells play a key role in the generation and maintenance of CD8+ Tcell responses. In this regard, CD8+ T cells primed in the absence ofCD4+ T cell (so-called “helpless” CD8+ T cells) are incapable ofmounting normal immune responses. Furthermore, chronic LCMV infection ismore severe in the absence of CD4+ T cells. Accordingly, helpless Tcells generated during LCMV-Cl-13 infection display an even moreprofound functional impairment than T cells generated in the presence ofCD4+ T cells. DbNP396-404 specific CD8+ T cells are deleted toundetectable levels, and DbGP33-41 and DbGP276-286 CD8+ T cellscompletely lose the ability to secrete IFN-γ and TNF-α.

CD4+ T cells were depleted at the time of LCMV-Cl-13 infection and micewere treated with anti-PD-L1 antibodies treatment from day 46 to day 60post-infection. LCMV-specific CD4+ T cells were not detectable byintracellular IFN-γ staining before or after treatment. Followingtreatment, treated mice had approximately 7 fold more DbGP276-286 CD8+ Tcells and 4 fold more DbGP33-41 CD8+ T cells in their spleen thanuntreated control mice (FIG. 3A). The number of virus-specific CD8+ Tcells in the spleen was also increased (FIG. 3B). This increase invirus-specific CD8+ T cells in treated mice was attributed to anincrease in proliferation, as detected by BrdU incorporation. 43% ofDbGP276-286 CD8+ T cells incorporated intermediate levels of BrdU and 2%incorporated high levels of BrdU in untreated mice, while 50%DbGP276-286 CD8+ T cells incorporated intermediate levels of BrdU and37% incorporated high levels of BrdU in treated mice. BrdU analysis wasperformed by introducing 1 mg/ml BrdU in the drinking water duringtreatment and staining was performed according to the manufacturer'sprotocol (BD Biosciences, San Diego, Calif.). Moreover, treated micecontained a higher percentage of CD8+ T cells expressing the cellcycle-associated protein Ki67 (60% versus 19% in untreated mice, FIG.3C). Response to treatment in CD8+ T cells in the PBMC was restricted tomice having high levels of CD8+ T cell expansion.

PD-1 inhibition also increased anti-viral cytokine production inhelpless, exhausted virus-specific CD8+ T cells. Following treatment,the number of DbGP33-41 and DbGP276-286 CD8+ T cells that produce IFN-γwas markedly increased (FIG. 4A), though higher numbers of DbNP396-404,KbNP205-212, DbNP166-175, and DbGP92-101 specific CD8+ T cells were alsodetected in treated mice (FIG. 4A). 50% of DbGP276-286 specific CD8+ Tcells from treated mice can produce IFN-γ compared to the 20% ofDbGP276-286 specific CD8+ T cells in control untreated mice. (FIG. 4B).Levels of IFN-γ and TNF-α produced by DbGP276-286 specific CD8+ T cellsfrom treated mice, however, were lower than fully functional DbGP276-286specific memory cells (FIG. 4C).

PD-1 inhibition also increased the lytic activity of helpless, exhaustedvirus-specific CD8+ T cells. Ex vivo lytic activity of virus-specificCD8+ T cells was detected following treatment, using a ⁵¹Cr releaseassay (Wherry et al., 2003. J. Virol. 77:4911-27). Viral titers werereduced by approximately 3 fold in the spleen, 4 fold in the liver, 2fold in the lung, and 2 fold in serum after 2 weeks of treatmentrelative to untreated mice (FIG. 4E).

These results therefore demonstrate that blocking the PD-1 pathwaybreaks CTL peripheral tolerance to a chronic viral infection, and thatexhausted CD8+ T cells deprived of CD4+ T cell help are not irreversiblyinactivated.

Example 2 Administration of Anti-Viral Vaccine and PD-1 Antagonist

One approach for boosting T cell responses during a persistent infectionis therapeutic vaccination. The rationale for this approach is thatendogenous antigens may not be presented in an optimal or immunogenicmanner during chronic viral infection and that providing antigen in theform of a vaccine may provide a more effective stimulus forvirus-specific T and B cells. Using the chronic LCMV model, mice wereadministered a recombinant vaccinia virus expressing the LCMV GP33epitope as a therapeutic vaccine (VVGP33), which resulted in a modestenhancement of CD8+ T cell responses in some chronically infected mice.Four out of the nine chronically infected mice that received thetherapeutic vaccine showed a positive response while none of the controlmice had a significant increase in the immune response against GP33.When this therapeutic vaccination was combined with a PD-L1 inhibitor,LCMV specific T cell responses were boosted to a greater level thancompared to either treatment alone and the effect of combined treatmentwas more than additive.

Example 3 Inhibition of the PD-1 Pathway in Chronically-Infected MiceUsing PD-1 RNAi

RNA interference (RNAi) is capable of silencing gene expression inmammalian cells. Long double stranded RNAS (dsRNAs) are introduced intocells and are next processed into smaller, silencing RNAs (siRNAs) thattarget specific mRNA molecules or a small group of mRNAs. Thistechnology is particularly useful in situations where antibodies are notfunctional. For example, RNAi may be employed in a situation in whichunique splice variants produce soluble forms of PD-1 and CTLA-4.

PD-1 silencer RNAs are inserted into a commercially available siRNAexpression vector, such as pSilencer™ expression vectors or adenoviralvectors (Ambion, Austin, Tex.). These vectors are then contacted withtarget exhausted T cells in vivo or ex vivo (see Example 4 below).

Example 4 Ex Vivo Rejuvenation of Exhausted T Cells

Virus-specific exhausted CD8+ T cells are isolated from LCMV-Cl-13chronically infected mice using magnetic beads or densitycentrifugation. Transfected CD8+ T cells are contacted with a monoclonalantibody that targets PD-L1, PD-L2 or PD-1. As described in Example 1,inhibition of the PD-1 pathway results in the rejuvenation of the CD8+ Tcells. Accordingly, there is an increase in CD8+ T cell proliferationand cytokine production, for example. These rejuvenated

CD8+ T cells are reintroduced into the infected mice and viral load ismeasured as described in Example 1.

Example 5 In vitro Screening of Novel CD8+ T Cell Rejuvenator Compounds

Compounds that modulate the PD-1 pathway can be identified in in vivoand ex vivo screening assays based on their ability to reverse CD8+ Tcell exhaustion resulting from chronic viral infection.

Exhausted CD8+ T cells are derived from mice chronically infected withLCMV-Cl-13 and next contacted with a test compound. The amount ofanti-viral cytokines (for example, IFN-γ or TNF-α) released from thecontacted T cell is measured, for example, by ELISA or otherquantitative method, and compared to the amount, if any, of theanti-viral cytokine released from the exhausted T cell not contactedwith the test compound. An increase in the amount of anti-viral cytokinereleased by treated cells relative to such amount in untreated cellsidentifies the compound as a PD-1 antagonist, useful to modulate T cellactivity.

Example 6 In Vivo Screening of Novel CD8+ T Cell Rejuvenator Compounds

Exhausted CD8+ T cells are derived from mice chronically infected withLCMV-Cl-13. A test compound is administered intravenously to theinfected mice. The amount of anti-viral cytokines (such as IFN-γ orTNF-α) that is released into the serum of treated and untreated mice ismeasured, for example, by ELISA or other quantitative method, andcompared. An increase in the amount of anti-viral cytokine found in theserum in treated mice relative to such amount in untreated miceidentifies the test compound as a PD-1 antagonist. Alternatively, theviral titer (e.g., serum viral titer) can be determined prior andsubsequent to treatment of the test compound.

Example 7 Chimpanzees as a Model for Immunotherapy of Persistent HCVInfection

Chimpanzees provide a model of HCV persistence in humans. Defects in Tcell immunity leading to life-long virus persistence both include adeficit in HCV-specific CD4+ T helper cells and impaired or altered CD8+T effector cell activity. Persistently infected chimpanzees are treatedwith antibodies against CTLA-4, PD-1, or a combination of the two. Theefficacy of blockade of the inhibitory pathways, combined withvaccination using recombinant structural and non-structural HCVproteins, and whether such strategies can enhance the frequency andlongevity of virus-specific memory T cells are determined. The defect inT cell immunity is exclusively HCV-specific in persistently infectedhumans and chimpanzees. The blood and liver of infected chimpanzees areexamined for expression of CTLA-4, PD-1, BTLA and their ligands and forthe presence of Treg cells. Antiviral activity may then be restored bydelivering to chimpanzees' humanized monoclonal antibodies that blocksignaling through these molecules.

Persistently infected chimpanzees are treated with humanized αCTLA-4antibodies (MDX-010, Medarex) or aPD-1 antibodies. The initial dose ofMDX-010 is 0.3 mg/kg followed 2 weeks later by 1.0 mg/kg and then 3, 10,30 mg/kg at three week intervals. After treatment with antibodies toco-inhibitory molecules, the humoral and cellular immune responses aswell as the HCV RNA load will be determined Samples are collected atweeks 1, 2, 3, 5, and 8, and then at monthly intervals. Samplesinclude: 1) serum for analysis of transaminases, autoantibodies,neutralizing antibodies to HCV, and cytokine responses, 2) plasma forviral load and genome evolution, 3) PBMC for in vitro measures ofimmunity, costimulatory/inhibitory receptor expression and function, 4)fresh (unfixed) liver for isolation of intrahepatic lymphocytes and RNA,and 5) fixed (formalin/paraffin embedded) liver for histology andimmunohistochemical analysis. Regional lymph nodes are also collected at2 or 3 time points to assess expression of co-inhibitory molecules andsplice variants by immunohistochemistry and molecular techniques.

To determine if vaccination with HCV antigens potentiates thetherapeutic effect of antibodies to PD-1, chimpanzees are treated asfollows: 1) intramuscular immunization with recombinant envelopeglycoproteins E1 and E2 (in MF59 adjuvant) and other proteins (core plusNS 3, 4, and 5 formulated with ISCOMS) at weeks 0, 4, and 24; 2)intramuscular immunization with the vaccine used in 1) butco-administered with αCTLA-4 antibodies (30 mg of each/Kg body weight,intravenously at weeks 0, 4, and 24 when vaccine is given); 3) identicalto 2) except that αPD-1 (or BTLA) antibodies are substituted for theCTLA-4 antibodies; 4) identical to Groups 2 and 3 except that acombination of CTLA-4 and PD-1 (or BTLA) antibodies are used in additionto the vaccine. HCV-specific T and B cell responses are monitored atmonthly intervals after immunization for a period of 1 year.

Markers examined on HCV-tetramer+ and total T cells in this analysisinclude markers of differentiation (e.g. CD45RA/RO, CD62L, CCR7, andCD27), activation (e.g. CD25, CD69, CD38, and HLA-DR),survival/proliferation (e.g. bcl-2 and Ki67), cytotoxic potential (e.g.granzymes and perforin), and cytokine receptors (CD122 and CD127). Aninteresting correlation exists between pre-therapy levels of thechemokine IP-10 and response to PEG IFN-γ/ribavirin. IP-10 levels aremeasured to investigate a potential correlation between negativeregulatory pathways or HCV-specific T cell responses and IP-10 levels.Expression of inhibitory receptors and ligands on PBMC are performed byflow cytometry.

Example 8 PD-1 Immunostaining in Reactive Lymphoid Tissue

Case material was obtained from the Brigham & Women's Hospital, Boston,Mass., in accordance with institutional policies. All diagnoses werebased on the histologic and immunophenotypic features described in theWorld Health Organization Lymphoma Classification system (Jaffe E S, etal. 2001) and in all cases diagnostic material was reviewed by ahematopathologist.

Immunostaining for PD-1 was performed on formalin-fixed paraffinembedded tissue sections following microwave antigen retrieval in 10 mMcitrate buffer, pH 6.0 with a previously described anti-human PD-1monoclonal antibody (2H7; 5), using a standard indirect avidin-biotinhorseradish peroxidase method and diaminobenzidine color development, aspreviously described (Jones D, et al. 1999; Dorfman D M, et al. 2003).Cases were regarded as immunoreactive for PD-1 if at least 25% ofneoplastic cells exhibited positive staining. PD-1 staining was comparedwith that of mouse IgG isotype control antibody diluted to identicalprotein concentration for all cases studied, to confirm stainingspecificity.

Monoclonal antibody 2H7 for PD-1 was used to stain formalin-fixed,paraffin-embedded specimens of reactive lymphoid tissue, thymus, and arange of cases of B cell and T cell lymphoproliferative disorders. Inspecimens of tonsil exhibiting reactive changes, including follicularhyperplasia, a subset of predominantly small lymphocytes in the germinalcenters exhibited cytoplasmic staining for PD-1, with infrequentPD-1-positive cells seen in the interfollicular T cell zones. The PD-1staining pattern in germinal centers was virtually identical to thatseen with an antibody to CD3, a pan-T cell marker, whereas an antibodyto CD20, a pan-B cell marker, stained the vast majority of germinalcenter B cells. Similar results were seen in histologic sections ofreactive lymph node and spleen. No PD-1 staining was observed in adultthymus.

Example 9 PD-1 Immunostaining in Paraffin Embedded Tissue Sections of BCell and T Cell Lymphoproliferative Disorders

A range of B cell and T cell lymphoproliferative disorders for PD-1expression were studied; the results are summarized in Table 4.Forty-two cases of B cell lymphoproliferative disorders were examinedfor PD-1 expression, including representative cases of precursor Blymphoblastic leukemia/lymphoblastic lymphoma, as well as a range oflymphoproliferative disorders of mature B cells, including a number of Bcell non-Hodgkin lymphomas of follicular origin, including 6 cases offollicular lymphoma and 7 cases of Burkitt lymphoma. None of the B celllymphoproliferative disorders showed staining for PD-1. In some cases,non-neoplastic reactive lymphoid tissue was present, and showed a PD-1staining pattern as seen in tonsil and other reactive lymphoid tissuenoted above.

Similarly, in 25 cases of Hodgkin lymphoma, including 11 cases ofclassical Hodgkin lymphoma and 14 case of lymphocyte predominant Hodgkinlymphoma, the neoplastic cells did not exhibit staining for PD-1.Interestingly, in all 14 cases of lymphocyte predominant Hodgkinlymphoma, the T cells surrounding neoplastic CD20-positive L&H cellswere immunoreactive for PD-1, similar to the staining pattern noted forCD57+ T cells in lymphocyte predominant Hodgkin lymphoma. ThesePD-1-positive cells were a subset of the total CD3+ T cell populationpresent.

A range of T cell lymphoproliferative disorders were studied forexpression of PD-1; the results are summarized in Table 4. Cases ofprecursor T cell lymphoblastic leukemia/lymphoblastic lymphoma, aneoplasm of immature T cells of immature T cells, were negative forPD-1, as were neoplasms of peripheral, post-thymic T cells, includingcases of T cell prolymphocytic leukemia, peripheral T cell lymphoma,unspecified, anaplastic large cell lymphoma, and adult T cellleukemia/lymphoma. In contrast, all 19 cases of angioimmunoblasticlymphoma contained foci of PD-1-positive cells that were alsoimmunoreactive for pan-T cell markers such as CD3. PD-1-positive cellswere consistently found at foci of expanded CD21+ follicular dendriticcells (FDC) networks, a characteristic feature of angioimmunoblasticlymphoma.

TABLE 4 PD-1 immunostaining in lymphoproliferative disorders PD-1immunostaining B cell LPDs  0/42* B-LL/LL 0/3 CLL 0/4 MCL 0/4 FL 0/6 MZL0/3 HCL 0/3 DLBCL 0/6 BL 0/7 LPL 0/3 MM 0/3 Hodgkin lymphoma  0/25Classical  0/11 Nodular lymphocyte predominant   0/14** T cell LPDs18/55 T-LL/LL 0/5 T-PLL 0/3 AIL 19/19 PTCL, unspecified  0/14 ALCL  0/12ATLL 0/3 Abbreviations: B-LL/LL—precursor B cell lymphoblasticlymphoma/lymphoblastic leukemia; CLL—chronic lymphocytic leukemia;MCL—mantle cell lymphoma; FL—follicular lymphoma; MZL—marginal zonelymphoma; HCL—hairy cell leukemia; DLBCL—diffuse large B cell lymphoma;BL—Burkitt lymphoma; LPL—lymphoplasmacytic lymphoma; MM—multiplemyeloma; T-LL/L—precursor T lymphoblastic leukemia/lymphoblasticlymphoma; T-PLL—T cell prolymphocytic leukemia; AIL—angioimmunoblasticlymphoma; PTCL—peripheral T cell lymphoma, unspecified; ALCL—anaplasticlarge cell lymphoma; ATLL—adult T cell leukemia/lymphoma. *number ofimmunoreactive cases/total number of cases **PD-1-positive cells formrosettes around neoplastic L&H cells in 14/14 cases

Example 10 General Methods for Studying PD-1 Expression on HIV-SpecificHuman CD8+ T Cells

The following methods were used to perform the experiments detailed inExamples 11-14.

Subjects:

Study participants with chronic Glade C HIV-1 infection were recruitedfrom outpatient clinics at McCord Hospital, Durban, South Africa, andSt. Mary's Hospital, Mariannhill, South Africa. Peripheral blood wasobtained from 65 subjects in this cohort, all of whom wereantiretroviral therapy naïve at the time of analysis. Subjects wereselected for inclusion based on their expressed HLA alleles matching theten class I tetramers that were constructed (see below). The medianviral load of the cohort was 42,800 HIV-1 RNA copies/ml plasma (range163-750,000), and the median absolute CD4 count was 362 (range129-1179). Information regarding duration of infection was notavailable. All subjects gave written informed consent for the study,which was approved by local institutional review boards.

Construction of PD-1 and PD-L1 Antibodies:

Monoclonal antibodies to human PD-L1 (29E.2A3, mouse IgG2b) and PD-1(EH12, mouse IgG1) were prepared as previously described and have beenshown to block the PD-1:PD-L1 interaction.

MHC Class I Tetramers:

Ten HIV MHC Class I tetramers, synthesized as previously described(Altman J D, et al. 1996), were used for this study: A*0205 GL9 (p24,GAFDLSFFL; SEQ ID NO:1), A*3002 KIY9 (Integrase, KIQNFRVYY; SEQ IDNO:2), B*0801 DI8 (p24, DIYKRWII; SEQ ID NO:3), B*0801 FL8 (Nef,FLKEKGGL; SEQ ID NO:4), B*4201 RM9 (Nef, RPQVPLRPM; SEQ ID NO:5), B*4201TL9 (p24, TPQDLNTML; SEQ ID NO:6), B*4201 TL10 (Nef, TPGPGVRYPL; SEQ IDNO:7), B*4201 YL9 (RT, YPGIKVKQL; SEQ ID NO:8), B*8101 TL9 (p24,TPQDLNTML; SEQ ID NO:9), and Cw0304 YL9 (p24, YVDRFFKTL; SEQ ID NO:10).

HLA Class I Tetramer Staining and Phenotypic Analysis:

Freshly isolated peripheral blood mononuclear cells (PBMC, 0.5 million)were stained with tetramer for 20 minutes at 37° C. The cells were thenwashed once with phosphate buffered saline (PBS), pelleted, and staineddirectly with fluorescein isothiosyanate (FITC)-conjugated anti-CD8(Becton Dickinson), phycoerythrin-conjugated anti-PD-1 (clone EH12), andViaProbe (Becton Dickinson). Cells were incubated for 20 minutes at roomtemperature, washed once in PBS, and resuspended in 200 μl PBS with 1%paraformaldehyde and acquired on a fluorescence-activated cell sorter(FACSCalibur™, Becton Dickinson). A minimum of 100,000 events wereacquired on the FACSCalibur™.

CFSE Proliferation Assays:

One million freshly isolated PBMC were washed twice in PBS, pelleted,and resuspended in 1 ml of 0.5 μM carboxy-fluorescein diacetate,succinimidyl ester (CFSE, Molecular Probes) for 7 minutes at 37° C. Thecells were washed twice in PBS, resuspended in 1 ml R10 medium (RPMI1640 supplemented with glutiathione, penicillin, streptomycin, and 10%fetal calf serum [FCS]), and plated into one well of a 24-well plate.Initial studies revealed that a final concentration of 0.2 μg/ml peptideyielded optimal proliferative responses, therefore this was the finalpeptide concentration in the well used for each assay. Negative controlwells consisted of PBMC in medium alone, or PBMC in medium with purifiedanti-PD-L1 (10 μg/ml), and positive control wells were stimulated with10 μg/ml of phytohemagluttinin (PHA). Following 6-day incubation in a37° C. incubator, the cells were washed with 2 ml PBS and stained withPE-conjugated MHC Class I tetramers, ViaProbe (Becton Dickinson), andanti-CD8-APC antibodies. Cells were acquired on a FACSCalibur andanalyzed by CellQuest® software (Becton Dickinson). Cells were gated onViaProbe-CD8+ lymphocytes. The fold increase in tetramer+ cells wascalculated by dividing the percentage of CD8+ tetramer+ cells in thepresence of peptide by the percentage of CD8+ tetramer+ cells in theabsence of peptide stimulation.

Statistical Analysis:

Spearman correlation, Mann-Whitney test, and paired t-test analyses wereperformed using GraphPad Prism Version 4.0a. All tests were 2-tailed andp values of p<0.05 were considered significant.

Example 11 PD-1 Expression on HIV-Specific CD8+ T Cells

A panel of 10 MHC Class I tetramers specific for dominant HIV-1 clade Cvirus CD8+ T cell epitopes was synthesized, based on prevalent HLAalleles and frequently targeted epitopes in Gag, Nef, Integrase, and RTallowing direct visualization of surface PD-1 expression on these cells.High resolution HLA typing was performed on the entire cohort, and asubset of 65 antiretroviral therapy naïve persons was selected for studybased on expression of relevant HLA alleles. A total of 120 individualepitopes were examined, and representative ex vivo staining of PD-1 onHIV tetramer+ cells is shown in FIG. 5A. PD-1 expression was readilyapparent on these tetramer+ cells, and was significantly higher than inthe total CD8 T cell population from the same individuals (p<0.0001); inturn, PD-1 expression on both tetramer+ CD8+ T cells and the total CD8+T cell population was significantly higher than in HIV-seronegativecontrols (FIG. 5B). For eight of the ten tetramers tested at least oneperson was identified in whom the level of expression onantigen-specific CD8+ cells was 100% (FIG. 5C). PBMC from 3 to 25individuals were stained for each HIV tetramer response, with medianPD-1 expression levels ranging from 68% to 94% of tetramer+ cells (FIG.5C). These findings were further confirmed by analysis of the meanfluorescence intensity (MFI) of PD-1 on both tetramer+ cells and thetotal CD8+ T cell population (FIG. 5B, C).

It was next determined whether there was evidence for epitope-specificdifferences in terms of PD-1 expression levels in persons with multipledetectable responses. Of the 65 persons examined, 16 individuals hadbetween 3 and 5 tetramer positive responses each. PD-1 expression wasnearly identical and approaching 100% for each response analyzed forthree of the sixteen subjects; however, the other 13 individualsdisplayed different patterns of PD-1 expression depending on the epitope(FIG. 5D). These data indicate that PD-1 expression may bedifferentially expressed on contemporaneous epitope-specific CD8+ Tcells from a single person, perhaps consistent with recent dataindicating epitope-specific differences in antiviral efficacy (TsomidesT J, et al. 1994; Yang O, et al. 1996; Loffredo J T, et al. 2005).

Example 12 The Relationship Between PD-1 Expression and HIV DiseaseProgression

The relationship was determined between PD-1 expression on HIV-specificCD8+ T cells and plasma viral load and CD4+ cell counts, both of whichare predictors of HIV disease progression. Consistent with previousstudies, the relationship between the number of tetramer positive cellsand viral load or CD4+ cell count failed to show any significantcorrelation (FIG. 6A, B). In contrast, there were significant positivecorrelations with viral load and both the percentage and MFI of PD-1expression on HIV tetramer positive cells (p=0.0013 and p<0.0001,respectively; FIG. 6A). There were also inverse correlations between CD4count and both the percentage and MFI of PD-1 on HIV tetramer positivecells (p=0.0046 and p=0.0150, respectively; FIG. 6B). Since thetetramers tested likely represent only a fraction of the HIV-specificCD8+ T cell population in these subjects, the relationship between PD-1expression on all CD8+ cells and these parameters was also examined.There were significant positive correlations between viral load and boththe percentage and MFI of PD-1 expression on the total CD8+ T cellpopulation (p=0.0021 and p<0.0001, respectively; FIG. 6C), and inversecorrelations were also observed between CD4+ cell count and both thepercentage and MFI of PD-1 expression on the total CD8+ T cellpopulation (p=0.0049 and p=0.0006, respectively; FIG. 6D). In this samegroup, PD-1 expression on CMV-specific CD8+ T cells was tested in 5subjects, and significantly less PD-1 was expressed on these cellscompared to HIV-specific CD8 T cells (median 23% CMV tetramer+ PD-1+,p=0.0036), and was not different than bulk CD8+ T cells in these sameindividuals, indicating that high PD-1 expression is not a uniformfeature of all virus-specific CD8+ T cells. These data suggestincreasing amounts of antigen in chronic HIV infection result inincreased expression of PD-1 on CD8+ T cells, and are consistent withmurine data in chronic LCMV infection, in which PD-1 expression isassociated with functional exhaustion of CD8+ T cells (Barber D L, etal. 2005). Moreover, they provide the first clear association, in alarge study including analysis of multiple epitopes, betweenHIV-specific CD8+ T cells and either viral load or CD4 count.

Example 13 The Relationship Between PD-1 Expression and CD8 T CellMemory Status and Function

PD-1 expression was next analyzed in the context of a number ofadditional phenotypic markers associated with CD8+ T cell memory statusand function, including CD27, CD28, CD45RA, CD57, CD62L, CD127, CCR7,perforin, granzyme B, and Ki67 (FIG. 7). Representative stainings forthese markers on B*4201 TL9 tetramer+ cells from one individual areshown in FIG. 7A, and aggregate data for 13 subjects are shown in FIG.7B. These studies were limited to those tetramer responses that weregreater than 95% PD-1 positive, as multiparameter flow cytometry ofgreater than 4 colors was not available in KwaZulu Natal. The HIVtetramer+ PD-1+ cells express high levels of CD27 and granzyme B, verylow levels of CD28, CCR7, and intracellular Ki67, low levels of CD45RAand perforin, and intermediate levels of CD57 and CD62L (FIG. 7B). Thesedata indicate that HIV-specific PD-1+ T cells display aneffector/effector memory phenotype, and are consistent with previousreports of skewed maturation of HIV-specific CD8+ T cells. In addition,virus sequencing was performed to determine whether these cells weredriving immune escape. Of 45 of these tetramer-positive responsesevaluated, the viral epitopes in only 5 were different from the SouthAfrican Glade C consensus sequence, indicating these cells exert littleselection pressure in vivo.

Previous experiments in mice using the LCMV model showed that in vivoblockade of PD-1/PD-L1 interaction by infusion of anti-PD-L1 blockingantibody results in enhanced functionality of LCMV-specific CD8+ T cellsas measured by cytokine production, killing capacity, proliferativecapacity, and, most strikingly, reduction in viral load. Short-term(12-hour) in vitro antigen-specific stimulation of freshly isolated PBMCfrom 15 HIV+ subjects, in the presence or absence of 1 μg/ml purifiedanti-PD-L1 antibody, failed to increase IFN-γ, TNF-α, or IL-2production.

Example 14 Effect of Blockading the PD-1/PD-L1 Pathway on Proliferationof HIV-Specific CD8+ T Cells

Because HIV-specific CD8+ T cells also exhibit impaired proliferativecapacity (2004), it was determined whether blockade of the PD-1/PD-L1could enhance this function in vitro. Representative data from aB*4201-positive individual are shown in FIG. 8A. Incubation of freshlyisolated CFSE-labeled PBMC with medium alone, or medium with anti-PD-L1antibody, resulted in maintenance of a population of B*4201-TL9-specificCD8+ T cells (1.2% of CD8+ T cells) that remained CFSEhi after six daysin culture. Simulation of CFSE-labeled PBMC for 6 days with TL9 peptidealone resulted in a 4.8-fold expansion of CFSElo B*4201 TL9 tetramer+cells, whereas stimulation of CFSE-labeled PBMC with TL9 peptide in thepresence of anti-PD-L1 blocking antibody further enhanced proliferationof TL9-specific cells, resulting in a 10.3-fold increase in tetramer+cells. CFSE proliferation assays were performed on 28 samples in thepresence and absence of purified anti-human PD-L1 blocking antibody. Asignificant increase in the proliferation of HIV-specific CD8+ T cellswas observed in the presence of peptide plus anti-PD-L1 blockingantibody as compared to the amount of proliferation followingstimulation with peptide alone (FIG. 8B; p=0.0006, paired t-test). Thefold increase of tetramer+ cells in the presence of anti-PD-L1 blockingantibody varied by individual and by epitope within a given individual(FIG. 8C), again suggesting epitope-specific differences in the degreeof functional exhaustion of these responses.

Example 15 Therapeutic Vaccination in Conjunction with Blocking PD-1Inhibitory Pathway Synergistically Improves the Immune Control ofChronic Viral Infection: A Concept Study of Combinatorial TherapeuticVaccine

The functional impairment of T cells including cytokine proliferation,cytolysis, and proliferation of antigen-specific T cells, is a definingcharacteristic of many chronic infections. Inactivated T cell immuneresponse is observed during a variety of different persistent pathogeninfections, including HIV, HBV, HCV, and TB in humans. T cellinactivation during chronic infection might correlate with the magnitudeand persistence of the antigen burden and originate from disruptedproximal T cell receptor signals, upregulation of inhibitory proteins ordown regulation of costimulatory proteins, and defects in accessory andcytokine signals. The defect in exhausted T cells is a primary reasonfor the inability of the host to eliminate the persisting pathogen.During chronic infection, exhausted virus specific CD8 T cellsupregulate two key inhibitory proteins: PD-1 and CTLA-4. An in vivoblockade of PD-1 increases the number and function of virus-specific CD8T cells and results in decreased viral load.

There are several drawbacks of current vaccination strategies forchronic viral infections. Specifically, effective boosting of antiviralCD8 T-cell responses is not observed after therapeutic vaccination. Inaddition, a high viral load and the low proliferative potential ofresponding T cells during chronic infection are likely to limit theeffectiveness of therapeutic vaccination. Thus, it is important todevelop therapeutic vaccine strategy to boost effectively the host'sendogenous T cell responses to control chronic infection.

A well-known chronic infection model induced by LCMV Clone-13 infectionwas used to determine the effectiveness of using a PD-1 antagonist incombination with a therapeutic vaccine. A vaccinia virus expressing GP33epitope of LCMV was used as a therapeutic vaccine to monitor anepitope-specific CD8 T cell immune response. A therapeutic vaccine wascombined with anti-PD-L1 antibody for blocking an inhibitory pathway inorder to investigate the synergist effect regarding a proliferation ofantigen-specific CD8 T cells and a resolution of persisting virus.

The following methods were used in these experiments:

Mice and Infections:

C57BL/6 mice (4- to 6-week-old females) were from The Jackson Laboratory(Bar Harbor, Me.). Mice were maintained in a pathogen-free vivariumaccording to NIH Animal Care guidelines. For the initiation of chronicinfections, mice were infected with 2×10⁶ PFU of LCMV clone-13 (CL-13)as described previously. Viral growth and plaque assays to determineviral titers have been described previously.

In Vivo Antibody Blockade and Therapeutic Vaccination:

Two hundred micrograms of rat anti-mouse PD-L1 (10F:9G2) wereadministered intraperitoneally every third day from 4 weekspost-infection with CL-13. At the time point of first treatment ofanti-PD-L1, 2×10⁶ PFU of recombinant vaccinia virus expressing theGP33-41 epitope (VV/GP33) as therapeutic vaccine or wild-type vacciniavirus (VV/WT) as control vaccine were given intraperitoneally.

Lymphocyte Isolation:

Lymphocytes were isolated from tissues and blood as previouslydescribed. Liver and lung were perfused with ice-cold PBS prior toremoval for lymphocyte isolation.

Flow Cytometry:

MHC class I peptide tetramers were generated and used as previouslydescribed. All antibodies were obtained from BD Pharmingen except forgranzyme B (Caltag), Bcl-2 (R&D Systems), and CD127 (eBioscience). Allsurface and intracellular cytokine staining was performed as described(Barber et al., Nature 439:682, 2006). To detect degranulation,splenocytes were stimulated for 5 h in the presence of brefeldin,monensin, anti-CD107a-FITC, and anti-CD107b-FITC.

Confocal Microscopy:

Spleens were removed from mice and frozen in OCT (TissueTek). From theseblocks, 10-20 mm cryostat sections were cut and fixed in ice-coldacetone for 10 minutes. For immunofluorescence, sections were stainedwith the following antibodies: ER-TR7 to detect reticular cells(Biogenesis, Kingston, N.H.) and polyclonal anti-LCMV guinea-pig serum.Stains were visualized with Alexa Fluor-488 goat anti-rat and AlexaFluor-568 goat anti-guinea-pig Ig (Molecular Probes) and analyzed byconfocal microscopy (Leica Microsystems AG, Germany). Images wereprepared using ImageJ (National Institutes of Health) and Photoshop(Adobe Systems Inc.).

The results demonstrated that a combination of therapeutic vaccine andanti-PD-L1 antibody displays a synergistic effect on proliferation ofantigen-specific CD8 T cells and resolution of persisting virus.Therapeutic vaccine could boost effectively a functionally restored CD8T cell population by blockade of PD-1/PD-L1 inhibitory pathway. Enhancedproliferation of antigen-specific CD8 T cells and accelerated viralcontrol were systematically achieved by combinatorial therapeuticvaccination (FIGS. 9A-9D and FIG. 10A-10D). Combinatorial therapeuticvaccine guides to a dramatic increase of functionally active CD8 T cells(FIG. 11A-D). In addition, therapeutic vaccine using vector expressingspecific epitope during blockade of PD-1/PD-L1 pathway enhances aproliferation of CD8 T cell specific to epitope encoded in vector (FIGS.9 and 11). The increased expression level of CD127 seen onantigen-specific CD8 T cells in the group treated with the combinatorialvaccine reflects the generation of a long-term memory T cell responses,while decreased expression levels of PD-1 and Granzyme B correlate toresolution of persisting virus (FIGS. 12A-12B).

There was a synergistic effect of therapeutic vaccine combined withPD-L1 blockade on restoration of function in ‘helpless’ exhausted CD8 Tcells (see (FIG. 13A-13E). Mice were depleted of CD4 T cells and theninfected with LCMV clone-13. Some mice were vaccinated with wild-typevaccinia virus (VV/WT) or LCMV GP33-41 epitope-expressing vaccinia virus(VV/GP33) at 7-wk post-infection. At the same time, the mice weretreated 5 times every three days with αPD-L1 or its isotype. Two weeksafter initial treatment of antibodies, mice were sacrificed foranalysis. The results are shown in FIG. 13A. The frequency of GP33specific CD8 T cells was also examined (FIG. 13B). Splenocytes werestimulated with GP33 peptide in the presence of αCD107a/b antibodies andthen co-stained for IFN-γ. The shown plots are gated on CD8-T cells(FIG. 13C). The percentage of IFN-γ⁺ cells after stimulation with GP33peptide per cells positive for Db-restricted GP33-41 tetramer was alsodetermined (FIG. 13D), as was the viral titer ((FIG. 13E). The resultsdemonstrate the synergistic effect of a vaccine combined with PD-1blockade.

These results show that combinations of blocking negative regulatorypathway and boosting CD8 T cells during chronic infection can be used inthe development of therapeutic vaccines to improve T cell responses inpatients with chronic infections or malignancies. Therapeuticinterventions, such as the use of an antagonist of PD-1, that boostT-cell responses and lower the viral load could increase disease-freesurvival and decrease transmission of the virus. Effective therapeuticvaccination could be used for chronic viral infections and persistingbacterial, parasitic infections. This strategy is also of use for thetreatment of malignancies.

Example 16 Enhancement of T Cell Immunotherapy Through Blockade of thePD1/PDL1 Pathway

It is important to develop strategies to treat and eliminate chronicviral infections such as the Human Immunodeficiency virus and HepatitisC. The CDC has recently reported that over one million American's areliving with HIV, exemplifying the need for more effective therapies. Itis important to determine how inhibitory signaling to lymphocytes cancontribute to a pathogen's ability to persistently evade the host immuneresponse.

The inhibitory immunoreceptor PD-1 (a member of the B7/CD28 family ofcostimulatory receptors) and its ligand (PD-L1) have been shown to bedramatically upregulated during states of chronic infection withlymphocytic choriomeningitis virus (LCMV). Additional studies using theLCMV model have demonstrated that blocking of the PD1/PDL1 pathwaysignificantly augments the endogenous anti-viral CD8 T cell responseduring the late phases of chronic infection when CD8 T cells areexhausted. Exhausted T cells are functionally compromised and do notmount effective immune responses upon antigen encounter. However,blockade of the PD1/PD-L1 pathway appears to reverse exhaustion andrestore their functional capacity. Data suggests that these effectspersist well beyond the immediate period of anti-PDL1 treatment.

The following experiments were performed in order to (1) assess theability of anti-PDL1 to enhance the proliferation and survivalanti-viral CD8 T cells upon adoptive transfer of immune (memory)splenocytes into congenitally infected (carrier) mice, (2) to evaluatethe functionality of virus-specific, memory CD8 T cells that haveexpanded in the presence of PD1/PDL1 blockade, and (3) to determine theexpression of various markers of differentiation in virus-specific CD8 Tcells that have expanded in the presence of PD1/PDL1 blockade.

The role of the PD-1 pathway was assessed in a well-developed model ofcyto-immune therapy for chronic viral infection. The model describedherein parallels that of T cell cyto-immune therapy for tumors in regardto the immunological barriers the limit the applicability of thesetherapies (such as corrupted or suppressed T cell/anti-tumor responses).Mice infected neonatally or in utero with LCMV do not mount endogenousLCMV-specific immune responses and go on to have high levels ofinfectious LCMV in blood and all tissues throughout their lives. Theseanimals are congenital carriers and are essentially tolerant to thepathogen. When splenocytes from an LCMV immune mouse are adoptivelytransferred into a congenital carrier the transferred immune memorycells rapidly undergo expansion and establish a vigorous immune responseagainst the virus. Approximately ⅔ of the animals receiving adoptivecyto-immune therapy go on to completely clear the infection when highdoses of splenocytes are transferred.

The following materials and methods were used in these experiments:

Mice and Infections.

4-6 week old female B57BL/6 mice were purchased from the JacksonLaboratory (Bar Harbor, Me.). Acute infection was initiated byintraperitoneal injection of 2×10⁵ PFU LCMV Armstrong. Congenitalcarrier mice were bred at Emory University (Atlanta, Ga.) from coloniesderived from neonatally infected mice (10⁴ PFU LCMV clone-13,intracerebral).

Adoptive Immunotherapy and In Vivo Antibody Blockade.

40×10⁶ whole splenocytes from LCMV immune mice (day 30-90post-infection) were isolated and transferred intravenously into 6-12week old LCMV carrier mice. 200 micrograms of rat-anti-mouse PD-L1(10F.9G2) were administered every 3^(rd) day for 15 days followingadoptive immunotherapy.

Flow Cytometry and Tetramer Staining.

MHC class I tetramers of H-2Db complexed with LCMV GP₃₃₋₄₁ weregenerated as previously described. All antibodies were purchased fromBD/Pharmingen (San Diego, Calif.). Peripheral blood mononuclear cellsand splenocytes were isolated and stained as previously described. Datawas acquired using a FACSCalibur™ flow cytometer (BD) and analyzed usingFlowJoe software (Tree Star Inc. Ashland, Oreg.)

Intracellular Cytokine Staining.

For intracellular cytokine staining 10⁶ splenocytes were cultured in thepresence or absence of the indicated peptide (0.2 μg/ml) and brefeldin Afor 5-6 hours at 37° C. Following staining for surface markers, cellswere permeabilized and stained for intracellular cytokines using theCytofix/Cytoperm preparation (BD/Pharmigen).

The following results were obtained:

Anti-PD-L1 Therapy Increases the Number of Virus Specific CD8 T Cells:

Peripheral blood mononuclear cells (PBMCs) were isolated from treated oruntreated animals on days 7, 11, 15, 22, and 35. Cells specific for theD^(b) GP33 epitope were assessed by tetramer staining. In twoindependent experiments it was found that animals treated withanti-PD-L1 therapy during the first 15 days following adoptive transferdeveloped significantly larger numbers of LCMV specific CD8 T cells whennormalized to the number of D^(b) GP33 positive cells per million PBMC's(FIG. 14). These data support the role of the PD-1/PD-L1 pathway inconferring some degree of proliferative suppression in normal memory Tcells. Moreover these results suggest that therapeutic inhibition ofthis pathway could augment the development and maintenance of thesecondary immune response generated following adoptive transfer into asetting of chronic infection with high antigen load.

PD-1/PD-L1 Blockade Enhances the Functionality of Antigen Specific CD8 TCells:

Spenocytes were isolated from treated and untreated animals on day 17post-adoptive transfer and analyzed for the expression of inflammatorycytokines (IFN-gamma and TNF alpha) or CD107ab (lysomal associatedmembrane protein, LAMP). Across all defined CD8 epitopes, IFN gammaexpression was found to be enhanced in animals receiving anti-PD-L1blockade compared to untreated animals (FIG. 15 a). Additionally,coexpression of IFN gamma and TNF alpha and CD107ab was also increasedfollowing anti-PD-L1 therapy (FIGS. 15B-15E). These findings indicatethat adoptively transferred memory splenocytes expanding in the presenceof PD-L1 blockade are functionally superior, in terms of inflammatorycytokine production and release of cytolytic granules, as compared tosplenocytes from untreated animals.

Example 17 Murine B Cell Responses During PD-1 Blockade

The following experiments were performed in order to determine whetherPD-1 blockade enhances B cell responses during chronic LCMV infection.Both B cell and T cell responses are critical in controlling chronicLCMV infection, thus improving B cell responses in chronic LCMV infectedmice may help lower viral load and enhance T cell function.

The following material and methods were used in these experiments:

Mice and Virus:

Four- to six-week-old female C57B1/6 mice were purchased from JacksonLaboratory (Bar Harbor, Me.). Prior to infection, chronic LCMV mice weredepleted of CD4 T cells by administration of gk1.5 antibody. Previousdata demonstrates that administration of 500 ug of gk1.5 days −2 and 0prior to viral challenge results in 95-99% decrease in the number of CD4T cells in the spleen and lymph node with the CD4 T cell numbers slowlyrecovering over 2 to 4 weeks. Mice received 2×10⁶ PFU of the Clone-13strain of LCMV intravenously on day 0 initiate chronic infection. Titersof virus were determined by a 6 day plaque assay on Vero cells.

Detection of ASC by ELISPOT:

Spleen and bone marrow single cell suspensions were depleted of redblood cells by 0.84% NH₄CL treatment and resuspended in RPMIsupplemented with 5% FCS. Antibody secreting cells were detected byplating cells onto nitrocellulose-bottom 96-well Multiscreen HAfiltration plates (Millipore). Plates were previously coated with 100 ulof 5 ug/ml of goat anti-mouse IgG+IgM+IgA (Caltag/Invitrogen) overnightat 4° C. Plates were then washed 3x with PBS/0.2% tween followed by 1×with PBS and blocked for 2 hours with RPMI+10% FCS to preventnon-specific binding. Blocking medium was replaced with 100 ul of RPMI5% FCS and 50 ul of 1×10⁷ cells/ml was plated in serial three-folddilutions across the plate. Plates were incubated for 6 hours at 37° C.and 5% CO₂. Cells were removed and plates were washed 3x with PBS and 3xwith PBS/0.2% tween. Wells were then coated with biotinylated goatanti-mouse IgG (Caltag/Invitrogen) diluted 1/1000 in PBS/0.2% tween/1%FCS and incubated overnight at 4° C. The secondary antibody was removedand plates were washed 3x with PBS/0.2% tween. Avidin-D HRP (Vector)diluted 1/1000 in PBS/0.2% tween/1% FCS was incubated for one hour atRT. Plates were washed 3x with PBS/0.2% tween and 3x with PBS anddetection was carried out by adding 100 ml of horseradishperoxidase-H₂O₂ chromogen substrate. The substrate was prepared byadding 150 ul of a freshly made AEC solution (10 mg of3-amino-9-ethylcarbazole (ICN) per ml dissolved indimethylformamide(Sigma)) to 10 ml of 0.1 M sodium acetate buffer pH4.8), filtering it through a 0.2-mm-pore-size membrane, and immediatelybefore use adding 150 ml of 3% H₂O₂. Granular red spots appeared in 3 to5 minutes, and the reaction was terminated by thorough rinsing with tapwater. Spots were enumerated with a stereomicroscope equipped with avertical white light.

Determination of Total Bone Marrow Cells:

For calculation of the total ASC response in bone marrow, the responsewas multiplied by the marrow cells of two femurs by a coefficient of7.9, since ⁵⁹Fe distribution studies have shown that 12.6% of totalmouse bone marrow is located in both femurs combined. No differenceshave been detected among the ASC activities of bone marrow cells fromthe femur, tibia, humorous, rib, or sternum. Typically, two adult femursyield 2.0×10⁷ to 2.5×10⁷ total bone marrow cells.

Flow Cytometry:

Directly conjugated antibodies were purchased from Pharmingen(anti-B220, anti-CD4, anti-CD138 anti-CD95, anti-Ki67, anti-IgDbiotinylated), or Vector labs (PNA). Strepavidin-APC was purchased fromMolecular Probes. All staining was carried out at 4° C. in PBSsupplemented with 1% FCS and 0.1% sodium azide. Cells were then fixed in2% formaldehyde (in PBS) and analyzed on a FACS Calibur using CellQuestsoftware (BD Biosciences).

Statistical Analysis:

Tests were performed using Prism 4.0 (GraphPad, San Diego, Calif.).Statistics were done using two-tailed, unpaired T test with 95%confidence bounds.

Total Numbers of Antibody Secreting Cells in the Spleen is EnhancedFollowing In-Vivo PD-1 Blockade:

Mice infected with LCMV Clone-13 were treated with anti (a)PD-L1approximately 60 days post infection. Mice were administered 200 ugαPD-L1 every third day for two weeks. At day 14 of αPD-L1 treatment, themice were sacrificed and the number of antibody secreting cells in thespleen was measured by ELISPOT and flow cytometric staining. In threeseparate experiments, mice treated with αPD-L1 showed significantlyincreased levels of antibody-secreting cells (ASC) in the spleen(p=0.011) as compared to untreated mice (FIG. 16 a). ASC can bedifferentiated from B cells in the spleen by their down-regulation ofthe B cell marker B220 and by expression of CD138 (syndecam-1). Inagreement with the ELISPOT results, increased numbers of B220^(low/int)CD138+ cells were seen in infected mice treated with αPD-L1 (FIG. 16 b).

Treatment of Chronic LCMV Infected Mice with αPD-L1 does not Lead toElevated Levels of Bone Marrow ASC.

It was determined whether antibody secreting cells within the bonemarrow were also enhanced during αPD-L1 treatment. The majority oflong-lived plasma cells reside within the bone marrow, and these plasmacells are critical to long-term maintenance of serum antibody levels.Chronic LCMV infected mice were treated with αPD-L1 approximately 60days post infection. Day 14 of αPD-L1 treatment, spleen and bone marrowASC levels were measured by ELISPOT. Although there were elevatednumbers of ASC in the spleen two weeks post-treatment, there was nochange in the numbers of ASC in the bone marrow at this time-point (FIG.17).

Co-Treatment of Chronic LCMV Infected Mice with αPD-L1 and ¹³⁷αCTLA-4Results in Synergistic Increases in Splenic ASC Levels:

It was further investigated whether blocking signaling with of anothernegative regulatory molecule, CTLA-4, would enhance the effect seenduring the PD-1 blockade. CTLA-4 binding to B7 is thought to bothcompete with the positive co-stimulatory molecule CD28 and/or providedirectly antagonizing TCR signals. Mice infected with LCMV Clone-13 weretreated with either treated with αPD-L1, αCTLA-4, both or leftuntreated, and two weeks post-treatment the levels of antibody secretingcells were measured by ELISPOT. Although treatment with αCTLA-4 showedno impact on ASC levels, co-treatment of αPD-L1 with αCTL-4 led to asynergistic increase in ASC above that seen with αPD-L1 treatment alone(FIG. 18).

Enhanced B Cell and CD4 T Cell Proliferation and Germinal CenterActivity in αPD-L1 Treated Mice:

Flow cytometric analysis of spleen populations in chronic mice treatedwith αPD-L1 showed enhanced levels of proliferation by increased Ki-67staining in both CD4 T cells and B cells. B cells within the germinalcenter reaction can be identified in the spleen by high levels of PNAand FAS staining. Following αPD-L1 treatment, there was a large increasein the frequency of PNA+FAS+B cells compared to untreated controls (FIG.19 a-19 b).

Example 17 PD-1 Expression on Human T Cells

CD8 T cells are essential for the control of many chronic infections. Asdisclosed herein, these CD8 T cells become exhausted following chronicantigenic stimulation, which is characterized by the induction of ahypoproliferative state and loss of the ability to produce anti-viralcytokines. Exhausted T cells have high expression of programmed death-1(PD-1) and, also PD-1 is upregulated by T cell activation and can betriggered by the PD-1 ligands, PD-L1 and PD-L2. It is disclosed hereinthat the PD-1 inhibitory pathway is an important mediator of CD8 T cellexhaustion during a chronic viral infection in mice. Virus specific CD8T cells maintained high levels of PD-1 expression in response to achronic infection, but not in response to an infection that issuccessfully eliminated. Blocking the interaction of PD-1/PD-L1interaction resulted in enhanced CD8 T cell proliferation, production ofanti-viral cytokines, and a reduction in viral load.

It was evaluated whether CD8 T cells specific for chronic infections inhumans express PD-1, and whether PD-1 blockade enhances CD8 T cellsresponses. This study (1) determined the expression pattern of PD-1 onsubsets of human peripheral blood mononuclear cells (PBMC): CD4, CD8, Bcell, NK, monocytes, DC; (2) Determined the phenotype of CD4 and CD8 Tcells that express PD-1; (3) determined PD-1 expression on chronicpersistent antigen [(Epstein-Barr virus (EBV and cytomegalovirus (CMV)]and acute resolved antigen (influenza and vaccinia)-specific cells; and(4) determined the effect of blocking PD-1/PD-L1 interaction on theproliferation of antigen-specific cells.

The following materials and methods were used in these studies:

Blood Samples:

Peripheral blood samples were obtained from 36 healthy individuals whowere seropositive for EBV, CMV, influenza or vaccinia viruses. Thesesubjects were selected based on their HLA allele expression matching HLAclass I tetramers specific for EBV, CMV, influenza or vaccinia virusproteins. PBMC were isolated from the blood samples overlymphocyte-separation medium (Cellgro, Herndon, Va.).

Antibodies, Peptides and Tetramers:

Phycoerythrin-conjugated anti-human PD-1 (EH12, mouse IgG1) andunconjugated human PD-L1 (29E.2A3, mouse IgG2b) were obtained. Directlyconjugated antibodies were obtained from Beckman Coulter, San Diego,Calif. (anti-CD3, CD11a, CD27, CD28, CD38, CD45RA, CD57, CD62L andgranzyme-B), BD Pharmingen, San Diego, Calif. (CD8, CD95, CD195, HLA-DR,Ki-67 and perforin), and R&D systems, Minneapolis, Mass. (CCR7).Peptides were made at the peptide synthesis lab at Emory University,Atlanta, Ga. The plasmid constructs expressing HLA-A2, -B7 and -B8 werekindly provided by the NIH Tetramer Core Facility, Atlanta, Ga. andAPC-labeled MHC class Upeptide tetramers carrying CTL epitopes of EBV(HLA-A2-GLCTLVAML (SEQ ID NO: 36), HLA-B8-RAKFKQLL (SEQ ID NO: 37) andFLRGRAYGL (SEQ ID NO: 38)), CMV(HLA-A2-NLVPMVATV (SEQ ID NO: 39),HLA-B7-TPRVTGGGAM (SEQ ID NO: 40)), influenza (HLA-A2-GILGFVFTL (SEQ IDNO: 41)) and vaccinia (HLA-A2-CLTEYILWV (SEQ ID NO: 42) and KVDDTFYYV(SEQ ID NO: 43)).

Immunophenotyping and CFSE Proliferation:

Heparinised human whole blood samples (200 ul) were stained withantibodies or tetramers and then analyzed (Ibegbu et al., J Immunol.174: 6088-6094, 2005) on a FACS Calibur using CellQuest software or on aLSRII flow cytometer using FACSDiva software (BD ImmunocytometrySystems). For CFSE assays, PBMC (2×10⁶/ml) were washed thoroughly andlabeled with 3 μM carboxy-fluorescein diacetate, succinimidyl ester(CFSE, Molecular Probes) at room temperature in dark for 5 min (see, forexample, Weston and Parish, J Immunol Methods 133:87-97, 1990). The CFSElabeled PBMC were stimulated with either peptide alone (1 μg/ml) orpeptide with anti-PD-L1 antibody (10 μg/ml). Control cultures consistedof either PBMC alone, PBMC with anti-PD-L1 antibody or PBMC with anisotype control antibody (IgG2b; 10 μg/ml). Following a 6-day incubationat 37° C., the cells were washed and stained with tetramer along withanti-CD3 and -CD8 antibodies extracellularly.

The following results were obtained:

Expression Pattern of PD-1 on PBMC Subsets:

PD-1 expression was examined on PBMC subsets in healthy individuals. Itwas observed that CD8+ T cells, CD4+ T cells and monocytes (CD14+)express high levels of PD-1, B cells (CD20+) express low levels of PD-1and NK cells (CD56+) and DC (CD11c+) do not express PD-1.

PD-1 is Preferentially Expressed Among Effector Memory CD8 and CD4 TCells:

CD8 T cells from normal healthy individuals were examined forco-expression of PD-1 with various phenotypic markers associated withdifferentiation state and function (FIG. 20A). In summary, naïve andcentral memory phenotype CD8 T cells only expressed low levels of PD-1,whereas CD8 T cells that expressed various markers associated witheffector/effector memory/or exhausted phenotype also expressed highlevels of PD-1 (FIG. 20B). These data suggested that PD-1 waspreferentially expressed among effector memory CD8 T cells. When the CD4T cells were examined we found similar trend (FIG. 20C).

PD-1 is Upregulated on Persistent Antigen-Specific Memory CD8 T Cells:

To evaluate whether CD8 T cells specific for chronic infections inhumans show increased expression of PD-1, PD-1 expression on memory CD8T cells specific for chronic persistent viruses (EBV and CMV) wascompared with acute virus specific T cells (influenza and vaccinia) in36 healthy individuals by staining with EBV-, CMV-, influenza- andvaccinia virus-specific tetramers (FIGS. 21A-21B). FIG. 21A showsrepresentative PD-1 GMFI of EBV, CMV, influenza and vacciniavirus-specific CD8 T cells. PD-1 expression was found to be increased onEBV-specific CD8 T cells than influenza (p=0.0335) and vaccinia(p=0.0036) virus-specific CD8 T cells (FIGS. 21A-21B). Similarly,CMV-specific CD8 T cells more frequently expressed PD-1 than influenza(p=0.0431) and vaccinia (p=0.019) (FIGS. 21A-21B). These results suggesta correlation between PD-1 expression and antigen experience.

Anti-PD-L1 Blockade Increases Proliferation of Chronic PersistentVirus-Specific CD8 T Cells:

It was assessed whether PD-1 blockade enhances persistentantigen-specific CD8 T cell responses similar to the results observed inmice.

CFSE labeled cells were stimulated with either EBV, CMV, influenza orvaccinia virus-specific peptides in the presence or absence ofanti-PD-L1 antibodies. After 6 days, the percentage oftetramer⁺CFSE^(lo) cells and CD8+ CFSE^(lo) cells was compared betweencultures that were stimulated with peptide alone and cultures that werestimulated with peptide and subsequently blocked with anti-PD-L1.Representative flow cytometry plots with proliferation of CMV andEBV-specific CD8 T cells are shown in FIG. 22A. Aggregated data from CMV(n=5), EBV (n=6), influenza (n=2) and vaccinia (n=2) seropositiveindividuals are shown in FIG. 22B. Blocking PD-1/PD-L1 interaction withanti-PD-L1 antibody resulted in increased proliferation of EBV andCMV-specific CD8 T cells whereas influenza and vaccinia virus-specificCD8 T cells did not show proliferation following blocking withanti-PD-L1. These results show that in the presence of peptide plusanti-PD-L1 blocking antibody, there is up to 3.5-fold increase in thefrequency of EBV or CMV-specific CD8 T cells compared to stimulationwith the peptide alone. It was assessed whether the proliferation ofantigen-specific CD8 T cells following anti-PD-L1 antibody blockade isrelated to the PD-1 expression by these cells. The data indicate apositive correlation between PD-1 expression and proliferation ofantigen-specific CD8 T cells (p=0.0083) (FIG. 22C).

Example 18 Liver Infiltrating Lymphocytes in Chronic Human HCV InfectionDisplay an Exhausted Phenotype with High PD-1 and Low CD127 Expression

The experiments described below document that chronic HCV infection,peripheral HCV-specific T cells express high levels of PD-1 and thatblockade of the PD-1/PD-L1 interaction led to an enhanced proliferativecapacity. Importantly, intrahepatic HCV-specific T cells not onlyexpress high levels of PD-1 but also decreased IL-7 receptor alpha(CD127), an exhausted phenotype that was HCV antigen specific andcompartmentalized to the liver, the site of viral replication.

Currently, no vaccine exists to prevent HCV infection and the onlylicensed therapy, alpha interferon (IFNα), either alone or incombination with the nucleoside analog ribavirin is expensive,associated with, at best, only a 50% clearance rate for the mostprevalent genotype (genotype 1) and complicated by significant sideeffects. The paucity of efficacious anti-HCV therapeutic optionshighlights the need for effective interventions aimed at augmenting orsupplementing the natural immune response that, alone or in concert withantiviral drug therapy, can prevent the detrimental consequences of HCVinfection.

Currently, little is known about the expression of PD-1 and its role inT cell exhaustion in chronic HCV infection, particularly at the site ofactive infection, the liver. The present study was undertaken to betterunderstand the T cell phenotype in HCV infection by measuring expressionof PD-1 on antigen-specific CD8+ T cells in both the liver andperipheral blood of patients with chronic HCV infection.

The following materials and method were used in these studies:

Subjects:

Seventeen patients with chronic HCV infection (HCV antibody and HCV PCRpositive) and negative for HIV by antibody screening were enrolled inthe study. All patients were naïve to HCV anti-viral therapies prior toenrollment. Seven of the fifteen patients were positive for HLA-A2 byFACS analysis. The patient characteristics are summarized in Table 5.

TABLE 5 Patient cohort demographic and clinical data Patient HLA- HCVBaseline Viral Identification Gender Age A2 Genotype Load (IU/ml) ALT153 HCV* M 43 + 2b 7,340,000 25 178 HCV* F 48 + 2 18,330,000 62 179 HCVM 54 − 1a 197,000 197 183 HCV F 56 + 1a 1,170,000 45 190 HCV M 52 − 1a5,990,000 27 193 HCV M 66 + 1a 16,120,000 30 601 HCV M 60 − 1b 4,690,00025 602 HCV M 48 − 1a 586,000 80 603 HCV M 58 + 1a 1,820,000 36 604 HCV M58 − 1a 2,850,000 57 605 HCV F 30 − 1 819,000 57 606 HCV M 50 − 1b591,000 18 607 HCV M 59 + 3a 343,000 31 608 HCV M 57 − 1b 395,000 16 609HCV M 55 + 1a 833,000 67 611 HCV M 53 − 1a 1,220,000 88 613 HCV M 59 −1b 6,160,000 40

HCV Antibody Testing, Viral Load Determination and Genotyping:

HCV antibody testing by ELISA was performed using a kit per themanufacturer's instructions (Abbott Diagnostics, Abbott Park, Ill.;Bio-Rad Laboratories, Hercules, Calif.). HCV viral load quantificationwas performed using a real-time RT-PCR assay (Roche Molecular Systems,Alameda Calif.). HCV genotyping was performed using a real-time RT-PCRassay (Abbott Diagnostics, Abbott Park, Ill.) and using a line probeassay (LIPA) (Bayer Diagnostics, Research Triangle Park, N.C.).

Peripheral Blood Mononuclear Cells:

EDTA and heparin anticoagulated blood (50-70 ml) was collected from eachpatient and either used directly for FACS staining or for PBMCisolation. PBMCs were isolated using Ficoll-Paque PLUS density gradient(Amersham, Oslo, Norway), washed twice in PBS, and either analyzedimmediately or cryopreserved in media containing 90% fetal calf serum(Hyclone) and 10% dimethyl sulfoxide (Sigma-Aldrich, St. Louis, Mo.).

Liver Biopsy:

Liver tissue was obtained by either ultrasound-guided needle biopsy orvia transjugular fluoroscopic technique and immediately put intoRPMI-1640 medium (Gibco) containing 10% fetal calf serum (Hyclone,Logan, Utah) for immunological assays. Another fragment was fixed informalin for histological examination.

Intrahepatic T Cell Isolation:

The liver biopsy sample obtained in RPMI-1640 medium (Gibco, Carlsbad,Calif.) containing 10% fetal calf serum (Hyclone, Logan, Utah) waswashed three times with the same media to remove cell debris and RBCs.Isolation of liver infiltrating lymphocytes was performed using anautomated, mechanical disaggregation system (Medimachine, BectonDickinson, San Jose, Calif.). The sample was inserted into a 50 μmMedicon and inserted into the Medimachine and run for 15 seconds.Dissagregated cells were removed using a syringe in the syringe port.The Medicon was rinsed twice with RPMI medium (Gibco, Carlsbad, Calif.)containing 10% fetal calf serum (Hyclone, Logan, Utah) to ensure maximumcell recovery. Cells were used immediately for FACS staining.

Antibodies, HLA-A2 Tetramers and Flow Cytometry:

Cells were stained with FITC, PE, PerCP and APC labeled monoclonalantibodies or tetramers according to the manufacturers' instructions andflow cytometry performed using FACS Calibur (Becton Dickinson, San Jose,Calif.). FACS data were analyzed with FlowJo software (Treestar). Thefollowing monoclonal antibodies from BD Pharmingen (BD Biosciences, SanJose, Calif.) were used: Anti-CD8 PerCP and anti-CD45RA APC. Anti-CD62LFITC, CD3 FITC and CD127 PE were obtained from Beckman Coulter(Fullerton, Calif.). Anti-PD-1 PE conjugated antibody (clone EH12) wasgenerated as described (Dorfman et al., Am. J. Surg. Pathol. 30:802-810,2006). HLA-A2 tetramers were specific for the following CD8+ T cellepitopes: HCV 1073: CINGVCWTV (SEQ ID NO: 44); HCV-1406: KLVALGINAV (SEQID NO: 45). Flow cytometric collection was performed on a FACSCaliber™(BD Biosciences, San Jose, Calif.) and analysis performed using FlowJosoftware (v8.1.1).

CFSE Labeling and Antibody Blockade:

10×0⁶ PBMCs were washed with PBS and labeled with 3 μM CFSE (MolecularProbes). Cells were adjusted to 1×10⁶ cells/ml and cultured in thepresence of 2 μg/ml of A2-HCV 1073 (CINGVCWTV, SEQ ID NO: 44) peptide.10U/ml of IL-2 were added on day 3 post stimulation. An unstimulatedcontrol was included in each assay. Specific blocking antibodies(anti-PD-L1; clone #29E and anti-PD-1; clone # EH12 (Dofman et al.,supra) were added to cell cultures at a concentration of 10 μg/ml at thetime of stimulation. Cells were incubated for 6 days, harvested andstained with surface antibodies and tetramers and analyzed by flowcytometry.

Statistical Analysis:

Results were graphed and analyzed using GraphPad Prism (v4). Comparisonsmade within the same patient were performed using paired t tests.Comparisons made between patients were made using unpaired t tests.

The following results were obtained:

PD-1 Expression on HCV Antigen Specific CD8+ T Cells:

Seventeen patients with HCV infection (all HIV negative) were studied(Table 1). Fifteen patients underwent both blood and liver sampling forphenotyping by flow cytometric analysis, and all were untreated withpharmacologic antiviral therapy prior to study enrollment. Sevenpatients in the cohort were HLA-A2 positive and demonstrated apopulation of HCV specific CD8+ T cells in the periphery by HLA tetramerstaining (Table 1). These HCV specific CD8+ T cells were evaluated forPD-1 expression (FIG. 23A). The level of PD-1 expression on total CD8+ Tcells in the peripheral blood from healthy donors was not significantlydifferent from that of the total pool of peripheral CD8+ T cells fromHCV infected patients (FIG. 23B). In contrast, the majority ofHCV-specific tetramer positive CD8+ T cells sampled from the peripheralblood were PD-1 positive (mean 85%, SEM 3.6) (FIG. 23A) withsignificantly higher expression than that of the total CD8+ T cellpopulation (p<0.0001) (FIG. 23B). Expression of differentiation,co-stimulatory, trafficking and effector function molecules on antigenspecific CD8+ T cells was also investigated. The HCV-specific tetramerpositive cells exhibit a memory phenotype (high CD11a, low CD45RA),early differentiation markers (high CD27, high CD28, intermediateexpression of CCR7 and CD62L) and low levels of mediators of effectorfunction granzyme B and perforin. Interestingly, these HCV tetramerpositive T cells in the peripheral blood expressed high levels of CD127(IL-7 receptor α chain), a phenotypic marker that when expressed at lowlevels identifies impaired memory T cell differentiation.

To determine whether the phenotype of CD8+ T cells was different in thesetting of non-chronic infection, Flu-specific T cells were examined infive healthy HLA-A2+ donors who were not infected with HCV. Thepercentage of peripheral Flu tetramer+ CD8+ T cells that expressed PD-1was 49% (SEM 14.1) (FIG. 23C). Five of the seven HLA-A2 positive chronicHCV patients were also identified by tetramer analysis to have Fluspecific CD8+ T cells. The percentage of Flu-specific T cells expressingPD-1 in these chronically infected HCV patients was not significantlydifferent from the same population in healthy donors (FIG. 23C).Importantly, because five of the seven HLA-A2+ HCV patients also haddetectable Flu specific CD8+ T cells, a comparison could be made, withineach patient, of PD-1 for T cells specific for a non-chronic (Flu) andchronic (HCV) infection. The difference between Flu-specific andHCV-specific T cell expression of PD-1 expression was significant (FIG.23C). The percentage of HCV specific CD8+ T cells expressing PD-1 (mean83%, SEM 6.4) was greater than the percentage of PD-1+ Flu specific CD8+T cells (49%, SEM 12.3) (p=0.048) (FIG. 23C).

PD-1 Expression on Human Peripheral Blood and Liver InfiltratingLymphocytes:

Peripheral blood and liver biopsies were analyzed for the expression ofPD-1 from fifteen patients chronically infected with HCV. Representativeflow cytometric analysis from five patients is shown in FIG. 24A.Whereas in the peripheral blood, 27% (SEM 3.4) of CD8+ T cells werePD-1+, the frequency of such cells was increased two fold (57%, SEM 3.6)in the liver (FIG. 24B). Hence, the liver is enriched in cellsexpressing high levels of PD-1. While naïve cells should express highlevels of both CD62L and CD45RA, in the liver the majority of CD8+ Tcells were CD62L low/CD45RA low consistent with a memory phenotype (FIG.24C). Analysis specifically of this memory population in both the liverand the periphery showed that PD-1 expression was elevated in the livercompared with the periphery (FIG. 24C). These data suggest that theincrease in the percentage of cells expressing PD-1 on the intrahepaticT cells is not merely due to the absence of the naïve population in thiscompartment. Rather, there is a preferential enrichment of PD-1+CD8+ Teffector memory (CD62L low/CD45RA low) cells within the liver comparedto the peripheral blood (FIG. 23C).

CD127 Expression on Human Peripheral Blood and Liver InfiltratingLymphocytes:

IL-7 is required for maintenance of memory CD8+ T cells (Kaech et al.,Nat Immunol 4:1191-8, 2003), and the alpha chain of its receptor, CD127,is downregulated on antigen specific T cells in persistent LCMV andgammaherpesvirus infections (see, for example, Fuller et al., J Immunol174:5926-30, 2005). This loss of CD127 during chronic infectioncorrelates with impaired cytokine production, increased susceptibilityto apoptosis, and a reduction in the ability of memory virus-specificCD8+ T cells to persist in the host. Accordingly, resolution of acutehepatitis B virus (HBV) infection correlates with upregulation of CD127expression and concomitant loss of PD-1 expression (Boettler et al., JVirol 80:3532-40, 2006). Interestingly, in the chronic HCV patients,only 20% (SEM 4.8) of total peripheral CD8+ T cells were CD127 negative,but in the hepatic CD8+ T cell infiltrates, this percentage increasedsignificantly to 58% (SEM 4.4) (FIG. 24D). Hence, the liver is enrichedin cells expressing an exhausted phenotype with high PD-1 and low CD127cells predominating. These data suggest that liver infiltrating CD8+ Tcells in chronic HCV patients do not phenotypically mirror theperipheral CD8+ T cell population. In the setting of HIV infection wherethe virus infects T cells and monocytes in the peripheral blood, lowlevels of CD127 are associated with functional or memory T cell defects(Boutboul et al., Aids 19:1981-6, 2005). In this study, the hepaticcompartmentalization of the cells showing this exhausted phenotypesuggests that the phenotype is intimately tied to the site of persistentviral replication.

PD-1 and CD127 Expression on HCV Antigen Specific CD8+ T Cells in theLiver:

Two of our HLA-A2 patients in the cohort also had an identifiable HCVspecific population by tetramer staining in the liver (FIG. 25).Expression of PD-1 and CD127 was directly compared on HCV specifictetramer positive CD8+ T cells in the liver versus the periphery ofthese individuals. HCV specific CD8+ T cells from the periphery weremostly PD-1 positive (mean 85%, SEM 3.6) and CD127 positive (mean 84%,SEM 4.0), while the hepatic HCV specific CD8+ T cells were mostly PD-1positive (mean 92%) but only rarely CD127 positive (mean 13%) (FIG. 25).At the site of viral replication, there appeared to be an expansion ofCD127 negative cells expressing high levels of PD-1. That peripheralantigen specific CD8+ T cells differentially express CD127 compared withthe intrahepatic compartment could be related to the level or timing ofantigen exposure needed to cause downregulation of CD127. In LCMVinfection of mice, exposure to persistent antigen load with chronicinfection, CD127 was persistently downregulated whereas short-livedexposure to LCMV antigen using GP33 only temporarily suppressed CD127expression and failed to induce T cell exhaustion (Lang et al., Eur JImmunol 35:738-45, 2005). Dependence on availability of antigen and timeof exposure was also observed to affect the expression of CD62L andCD127, whereas persistent antigen led to persistent downregulation ofboth CD62L and CD127 (Bachmann et al., J Immunol 175:4686-96, 2005).Without being bound by theory, in chronic HCV infection, the few HCVspecific CD8+ T cells detected in the periphery may not be continuouslyexposed to sufficient antigen to maintain low levels of CD127. Thus, theT cells may “believe” that the virus has been cleared.

Blockade of PD-1/PD-L1 Leads to Increased Expansion of HCV SpecificTetramer Positive CD8+ T Cells:

Evidence from the patient population suggests that blockade of thePD-1/PD-L1 interaction with anti-PD-L1 or anti-PD-1 antibody increasesthe proliferative capacity of HCV-specific T cells (FIG. 26). Additionof blocking antibodies in the presence of IL-2 and HCV-specific peptideresulted in a four-fold increase in expansion of the HCV-specific Tcells as demonstrated by monitoring the frequency of carboxyfluoresceinsuccinimidyl ester (CFSE)^(low) tetramer labeled CD8+ T cells afterstimulation with cognate peptide for 6 days.

The results show that at the site of infection, the liver, the frequencyof HCV specific CD8+ T cells expressing PD-1 is high. Second, themajority of HCV specific CD8+ T cells from the peripheral blood ofpatients with chronic HCV infection express high levels of CD127. Thephenotype of T cells in chronic HCV infection was characterized bystudying the expression of the PD-1 molecule linked to impaired effectorfunction and T cell exhaustion. The results show that the majority ofHCV specific T cells in the intrahepatic compartment express PD-1 butlack CD127, a phenotype consistent with T cell exhaustion. Thus, PD-1antagonists are of use as therapeutic agents for the treatment of HCVinfection.

Example 19 PD1 Blockade Induces Expansion of SIV-Specific CD8 Cells InVitro

Anti-viral CD8 T cells play a critical role in the control of HIV/SIVinfections. A central role for CD8 T cells has been shown by viralre-emergence during transient in vivo depletions in SIV-infectedmacaques. Consistent with this, contemporary vaccine strategies designedto elicit high frequencies of anti-viral CD8 T cells have containedpathogenic SHIV and SIV challenges in macaques (see, for example Barouchet al., Science 290, 486-92 (2000); Casimiro et al., J Virol 79,15547-55 (2005).

Both the function and the frequency of anti-viral CD8 T cells arecrucial for the control of chronic viral infections such as HIV(Migueles et al. Nat Immunol 3, 1061-8, 2002) and Lymphocyticchoriomeningitis virus (LCMV). Effective anti-viral CD8 T cells possessa number of functional properties including the ability to producedifferent cytokines, cytotoxic potential, and high proliferativepotential and low apoptosis. In chronic viral infections virus-specificCD8 T cells undergo exhaustion that is associated with the loss of manyof these functions (Zajac et al., J Exp Med 188, 2205-13, 1998).Similarly, HIV-specific CD8 T cells from individuals with progressivedisease have been shown to be impaired for their function. These CD8 Tcells can produce cytokines such as IFN-γ but are impaired for theproduction of IL-2, a cytokine that is critical for the T cellproliferation and survival; expression of perforin (Appay et al., J ExpMed 192, 63-75, 2000, a molecule that is critical for cytolyticfunction; and proliferative capacity, a property that has beenimplicated to be critical for the control of HIV (see, for example,Harari et al., Blood 103, 966-72, 2004) and SIV. HIV-specific T cellsexpress high levels of PD-1 and this expression is directly proportionalto the level of viremia. A transient blockade of interaction betweenPD-1 and PD-L1 in vitro restores HIV-specific T cell function.

The expression of PD-1 on SIV-specific CD8 T cells following infectionwith a pathogenic SIV239 in macaques was investigated. The resultsdemonstrate that SIV-specific CD8 T cells express high levels of PD-1and blockade of PD-1:PDL-1 pathway in vitro results in enhancedexpansion of these cells. The following results were obtained:

Elevated PD-1 Expression on SIV-Specific CD8 T Cells Following SIV239Infection:

The level of PD-1 expression on CD8 T cells from normal healthy andSIV-infected macaques was investigated to understand the role of PD-1expression and its relationship with the control of SIV-infection. Asignificant proportion (40-50%) of total CD8 T cells from normal healthymacaques expressed PD-1 (FIG. 27A). The PD-1 expression waspredominantly restricted to memory cells and was absent on naïve CD8 Tcells. A similar PD-1 expression pattern was also observed for total CD8T cells from SIVmac239-infected macaques (FIGS. 27B and C). However, themajority (>95%) of SIV Gag CM9-specific CD8 T cells were positive forPD-1 expression and a significant proportion of these cells further upregulated PD-1 expression (MFI of 580) compared to total CD8 T cells(MFI of 220) (FIG. 27D). Collectively, these results demonstrate that asignificant proportion of memory CD8 T cells from normal andSIV-infected macaques express PD-1 and the level of PD-1 expression isfurther elevated on the SIV-specific CD8 T cells.

In Vitro Blockade of PD-1 Results in Enhanced Expansion of SIV-SpecificCD8 T Cells:

To study the effect of PD-1 blockade on the function of SIV-specific CD8T cells, proliferation assays were conducted in the presence and absenceof a blocking antibody to human PD-1 molecule that is cross reactive tomacaque PD-1. PBMC from Mamu A*01 positive rhesus macaques that wereinfected with a pathogenic simian and human immunodeficiency virus 89.6P(SHIV 89.6P) were stimulated with P11C peptide (Gag-CM9 epitope) in theabsence and presence of anti-PD-1 blocking Ab for six days. Thefrequency of Gag CM-9 tetramer positive cells was evaluated at the endof stimulation. Unstimulated cells served as negative controls. As canbe seen in FIG. 28A-28B, stimulation with P11C peptide resulted in anabout 4-80 fold increase in the frequency of tetramer positive cells. Inaddition, in four out of six macaques tested, stimulations with P11Cpeptide in the presence of anti-PD-1 blocking Ab resulted in about 2-4fold further enhancement in the frequency of tetramer positive cellsover stimulations with P11C peptide in the absence of blocking antibody.

These results demonstrate that PD-1 blockade enhances the proliferativecapacity of SIV-specific CD8 T cells in SIV-infected macaques.

Example 20 Role of PD-L2

Two PD-1 ligands differ in their expression patterns: PD-L1 isconstitutively expressed and upregulated to higher amounts on bothhematopoietic and nonhematopoeitic cells, whereas PD-L2 is onlyinducibly expressed on dendritic cells (DCs) and macrophages. Althoughsome studies for evaluating the role that PD-L2 plays in T cellactivation have demonstrated inhibitory function for PD-L2, otherstudies reported that PD-L2 stimulate T cell proliferation and cytokineproduction. To delineate the role of PD-L2 on T cell immune response,the kinetics of PD-L2 expression on different cell types ex vivo wasexamined after LCMV Armstrong infection (FIG. 29). In contrast to PD-L1expression, PD-L2 expression was expressed limitedly on DC during a veryshort time (day 1-4 post-infection). This result suggests that PD-L2expression is closely related to DC regulation and results in regulationof T cell activation.

Example 21 PD-1 is Expressed by the Majority of Effector Memory CD8 TCells in the Blood of Healthy Humans

PD-1 expression on CD3+/CD8+ T cells from the blood of healthy humanadults was investigated. In human blood 20-60% of CD8 T cells expressedPD-1. The relationship between T cell differentiation state and PD-1expression was examined. CD3+/CD8+ T cells were delineated into naïve,central memory (T_(CM)), effector memory (T_(EM)), and terminallydifferentiated effector (T_(EMRA)) subsets based on patterns of CD45RAand CCR7 expression. PD-1 was not expressed by naïve T cells, and byapproximately one third of T_(CM) and T_(EMRA). In contrast, 60% ofT_(EM) expressed PD-1. These data demonstrate that the majority ofT_(EM) isolated from the blood of healthy human adults express PD-1.

Based on these analyses, T cells were subdivided into multiplepopulations based on CD45RA and CCR7 expression. An additionalrelationship was found between CD45RA expression and PD-1 expression.Specifically, CCR7−/CD8+ T cells with the lowest CD45RA expressioncontained the highest proportion of PD-1+ cells. In conclusion, PD-1 waspredominantly expressed by T_(EM), to a lesser extent by T_(EMRA) andT_(CM), and was not expressed among naïve CD8 T cells. These dataillustrate that a large proportion of T_(EM) CD8 T cells express PD-1among healthy human adults.

To characterize the properties of PD-1+ CD8 T cells further, theco-expression of PD-1 and several T cell differentiation markers wasexamined. The majority of PD-1+ CD8 T cells bore markers associated withantigen experience and effector/effector memory differentiation. Forinstance, CD11a+/CCR7−/CD62L−/CD45RA−/KLRG1+/granzyme B+/perforin+CD8 Tcells were enriched in PD-1 expression. In contrast, naïve phenotype(CD11a−/CCR7+/CD62L+/CD45RA+/KLRG1−) CD8 T cells expressed low levels ofPD-1. Thus, PD-1 was preferentially expressed on antigen-experienced CD8T cells with effector/effector memory qualities.

Example 22 PD-1 is Expressed by the Majority of Effector Memory CD4 TCells in Blood of Healthy Humans

PD-1 expression among CD3+CD4+ T cells was then investigated. Thirtypercent of CD4 T cells expressed PD-1 in the blood of healthy adults.Similar to CD8 T cells, naïve CD4 T cells expressed little PD-1. While aminority of T_(CM) CD4 T cells expressed PD-1, PD-1 expression waspreferentially enriched among T_(EM) CD4 T cells (50%).

To further characterize the properties of CD4 T cells that expressed PD,CD4+/CD3+ T cells were assayed from the blood of healthy individuals forthe co-expression of PD-1 and several T cell differentiation markers.Similar to CD8 T cells, PD-1 expression was enriched on CD4 T cells withan effector/effector memory phenotype, including CD62L−, CD95+, CD45RA−,CCR7−, and CCR5+ cells.

Example 23 PD-1 is More Highly Expressed on CD8 T Cells Specific for EBVand CMV Infections in Humans

To test whether PD-1 expression is correlated with viral antigenpersistence, PD-1 expression was compared on EBV, CMV, influenza, andvaccinia virus specific CD8 T cells. EBV and CMV-specific CD8 T cellsexpressed high levels of PD-1. In contrast, influenza virus specificmemory CD8 T cells expressed intermediate levels of PD-1 and vacciniavirus specific CD8 T cells express low levels of PD-1. Hence memory CD8T cells specific for chronic infections (EBV and CMV) expressed higherlevels of PD-1 than acute (influenza and vaccinia) infections. Theseresults show that CD8 T cells specific for chronic infections (EBV andCMV) expressed higher levels of PD-1 than acute infections (influenzaand vaccinia viruses). CD8 T cells specific for very common chronicinfections can express high levels of PD-1.

Example 24 Anti-PD-L1 Blockade Increases Proliferation of CD8 T CellsSpecific for EBV and CMV Infections in Humans

Blockade of the PD-1 inhibitory pathway results in enhanced clonalexpansion of HIV-specific CD8 T cells upon in vitro stimulation. As CD8T cells specific for common chronic infections also express PD-1, it wastested whether blockade of the PD-1/PD-L1 pathway could enhance theproliferation of CD8 T cells specific for EBV, CMV, and also vacciniavirus (an acute infection resulting in PD-1 memory CD8 T cells).Lymphocytes were isolated from the blood of individuals containing CD8 Tcells specific for CMV, EBV, or VV were labeled with CFSE and culturedfor 6 days under various conditions. As expected, incubation of freshlyisolated peripheral blood mononuclear cells (PBMC) with medium alone, ormedium with anti-PD-L1 antibody, did not induce proliferation ofvirus-specific CD8 T cells. Stimulation of PBMC for 6 days withvirus-derived peptides resulted in division of tetramer+ CD8 T cells.However, peptide stimulation of PBMC in the presence of anti-PD-L1blocking antibody further enhanced division of EBV and CMV-specific CD8T cells, resulting in a greater fold-expansion than peptide alone Theenhanced division induced by anti-PD-L1 blocking antibody varied amongindividuals and even among different epitopes within a given individual.Moreover, PD-1 blockade did not result in enhanced expansion of vacciniaor influenza specific CD8 T cells. The degree of enhanced divisioninduced by blocking PD-L1 in culture could be related to the amount ofPD-1 expressed by antigen specific CD8 T cells prior to stimulation.These data suggest that PD-1 expression on CD8 T cells specific forchronic infections inhibits their proliferative capacity upon antigenicstimulation.

Example 25 Sustained PD-L1 Blockade Further Increases Proliferation ofCD8 T Cells Specific for Chronic Infections

Upon in vitro stimulation, the addition of PD-L1 blocking antibody ledto increased division among CD8 T cells specific for EBV and CMV.Anti-PD-L1 mAb was added once (day 0), and proliferation was assessed atthe end of the six-day culture period. In vivo anti-PD-L1 treatment inmice involved multiple injections of blocking antibody. Furthermore, inthese murine studies, in vivo PD-L1 blockade resulted in a rapidupregulation of PD-1 expression among CD8 T cells specific for chronicviral antigen. For these reasons, it was tested whether repeatedadditions of anti-PD-L1 to stimulated T cell cultures would furtherenhance proliferation. The addition of a-PD-L1 mAb on days 0, 2, and 4of culture resulted in an even greater accumulation of EBV specific CD8T cells than a single addition of mAb at day 0. Similar data wasobserved for CMV specific CD8 T cells. These data suggest that continuedblocking of PD-1 signaling can optimize the ability to increase thenumbers of CD8 T cells specific for chronic antigens.

Example 26 Additional Methods for Studies Described in Example 27

Study Group:

Fourteen Indian rhesus macaques (Macaca mulatta) infected with SIV werestudied. Eight macaques were used for the early chronic phase and wereinfected intravenously with 200 TCID50 of SIV251. Six macaques were usedfor the late chronic phase, three were infected with SIV251intrarectally and three were infected with SIV239 intravenously. Allmacaques, except RDb11, were negative for Mamu B08 and Mamu B17 alleles.RDb11 was positive for Mamu B17 allele.

In Vivo Antibody Treatment:

Macaques were infused with either partially humanized mouse anti-humanPD-1 antibody (clone EH12-1540) (Dofrman et al., Am J Surg Pathol 30,802-810 (2006)) or a control antibody (SYNAGIS). The anti-PD-1 antibodyhas mouse variable heavy chain domain linked to human IgG1 (mutated toreduce FcR and complement binding) (Xu et al., Cell Immunol 200, 16-26(2000)) and mouse variable light chain domain linked to human K. Theclone EH12 binds to macaque PD-1 and blocks interactions between PD-1and its ligands in vitro (Velu et al., J Virol 81, 5819-5828 (2007).SYNAGIS is a humanized mouse monoclonal antibody (IgG1κ) specific to Fprotein of respiratory syncytial virus (Medimmune). Antibodies wereadministered intravenously at 3 mg kg⁻¹ of body weight on days 0, 3, 7and 10.

Immune Responses:

Peripheral blood mononuclear cells from blood and lymphocytes fromrectal pinch biopsies were isolated as described previously (Velu etal., J Virol 81, 5819-5828 (2007). Tetramer staining (Amara et al.,Science 292, 69-74 (2001)), intracellular cytokine production(Kannanganat et al., J Virol 81, 8468-8476 (2007)) and measurements ofanti-SIV Env binding antibody (Lai et al., Virology 369, 153-167 (2007))were performed as described previously.

B Cell Responses:

A total of 100 μl of blood was surface stained with antibodies to CD3(clone SP34-2, BD Biosciences), CD20 (2H7, e-Biosciences), CD21 (B-ly4,Becton Dickson) CD27 (M-T2712, Becton Dickson) and PD-1 (clone EH-12),each conjugated to a different fluorochrome. Cells were lysed and fixedwith FACS lysing solution, and permeabilized using FACS perm (BDBiosciences) according to the manufacturer's instructions. Cells werethen stained for intracellular Ki67 using an anti-Ki67 antibodyconjugated to phycoerythrin (PE) (clone B56, Becton Dickson). Afterstaining, cells were washed and acquired using LSRII (BD Biosciences),and analysed using FLOWJO™ software.

Titres of Anti-PD-1 Antibody and Monkey Antibody Response AgainstAnti-PD-1 Antibody in Serum:

To measure the levels of anti-PD-1 antibody, plates were coated withgoat anti-mouse immunoglobulin (pre-absorbed to human immunoglobulin,Southern Biotech), blocked and incubated with different dilutions ofserum to capture the blocking antibody. Bound antibody was detectedusing anti-mouse IgG conjugated to HRP (pre-absorbed to humanimmunoglobulin, Southern Biotech). Known amounts of blocking antibodycaptured in the same manner were used to generate a standard curve. Tomeasure the levels of monkey antibody response against the anti-PD-1antibody, plates were coated with anti-PD-1 antibody (5 μg ml⁻¹),blocked and incubated with different dilutions of serum to capture theanti-blocking antibody. Bound antibody was detected using anti-humanλ-chain-specific antibody conjugated to HRP (Southern Biotech). Thisdetection antibody does not bind to the blocking antibody because onlythe constant regions of the heavy and light chains were humanized andthe constant region of light chain is κ. The amount of captured monkeyimmunoglobulin was estimated using a standard curve that consisted ofknown amounts of purified macaque immunoglobulin that had been capturedusing anti-macaque immunoglobulin.

Quantification of SIV Copy Number:

SIV copy number was determined using a quantitative real-time PCR aspreviously described (Amara et al., Science 292, 69-74 (2001)). Allspecimens were extracted and amplified in duplicates, with the meanresult reported.

Amplification and Sequencing of the Tat TL8 Epitope:

A 350-nucleotide fragment including Tat TL8 epitope was amplified bylimiting dilution RT-PCR. Viral RNA was extracted using the QIAAMP™Viral RNA mini kit (Qiagen) from plasma. vRNA was reverse transcribedwith the SIVmac239-specific primer Tat-RT3(5′-TGGGGATAATTTTACACAAGGC-3′) and Superscript III (Invitrogen) usingthe manufacturer's protocol. The resultant cDNA was diluted and copynumber was determined empirically in our nested PCR protocol. Limitingdilution, nested PCR was performed at ˜0.2 copies per reaction using theExpand HiFi PCR kit (Roche Applied Sciences) with the following primers:

Outer Primers:

(SEQ ID NO: 53) Tat-F1 (5′-GATGAATGGGTAGTGGAGGTTCTGG-3′) (SEQ ID NO: 54)Tat-R2 (5′-CCCAAGTATCCCTATTCTTGGTTGCAC-3′)

inner Primers:

(SEQ ID NO: 55) Tat-F3 (5′-TGATCCTCGCTTGCTAACTG-3′)  (SEQ ID NO: 56)Tat-R3 (5′-AGCAAGATGGCGATAAGCAG-3′).The first round reactions were cycled using the following program: 94°C. for 1 min, followed by 10 cycles of 94° C. for 30 s, 55° C. for 30 s,and 68° C. for 1 min, followed by 25 more cycles identical to the firstten but for the addition of 5 s to the extension time at every cycle,followed by a final extension at 68° C. for 7 min. The second roundreactions were cycled using the following programme: 94° C. for 1 min,followed by 35 cycles of 94° C. for 30 s, 53° C. for 30 s, and 68° C.for 1 min, followed by a final extension at 68° C. for 7 min. Afterclean-up with ExoSap-IT (USB Corporation), PCR products were sequenceddirectly using the inner primers on an automated sequencer. Contigs wereassembled using Sequencher 4.8 (Gene Codes Corporation). Ampliconscontaining nucleotides with double chromatogram peaks were excluded.

Statistical Analyses:

Linear mixed effects models were used to determine differences in bloodchemistry and complete blood count values betweenanti-PD-1-antibody-treated and control-antibody-treated animals. TheBonferroni method was used to adjust P values for multiple tests. Apaired t-test was used for comparison of immune responses before andafter PD-1 blockade. Log-transformed data were used when the data werenot normal, but log-normal. A Wilcoxon rank-sum test was used to comparethe fold reductions in viral loads between the groups. A Mantel-Haenszellog rank test was used to compare the survival curves between thegroups. Statistical analyses were performed using S-PLUS 8.0. Atwo-sided P<0.05 was considered statistically significant.

Example 27 Proliferation of Memory B Cells Induced by PD-1 Blockade

Chronic immunodeficiency virus infections are characterized bydysfunctional cellular and humoral antiviral immune responses. As such,immune modulatory therapies that enhance and/or restore the function ofvirus-specific immunity may protect from disease progression. The safetyand immune restoration potential of blockade of the co-inhibitoryreceptor programmed cell death 1 (PD-1) during chronic simianimmunodeficiency virus (SIV) infection was investigated in macaques. Itwas demonstrated that PD-1 blockade using an antibody to PD-1 is welltolerated and results in rapid expansion of virus-specific CD8 T cellswith improved functional quality. This enhanced T-cell immunity was seenin the blood and also in the gut, a major reservoir of SIV infection.PD-1 blockade also resulted in proliferation of memory B cells andincreases in SIV envelope-specific antibody. These improved immuneresponses were associated with significant reductions in plasma viralload and also prolonged the survival of SIV-infected macaques. Blockadewas effective during the early (week 10) as well as late (week 90)phases of chronic infection even under conditions of severe lymphopenia.These results demonstrate enhancement of both cellular and humoralimmune responses during a pathogenic immunodeficiency virus infection byblocking a single inhibitory pathway and identify a novel therapeuticapproach for human immunodeficiency virus/acquired immunodeficiencysyndrome, and demonstrate that monitoring B cell response can be used toassess the efficacy of therapy.

Virus-specific T cells show varying degrees of functional impairmentduring chronic infections (Wherry et al., Immunity 27, 670-684 (2007);Klenerman et al., Nat Immunol 6, 873-879 (2005)). Although these T cellsretain some antiviral functions, they are less polyfunctional comparedwith antiviral T cells seen in acute infections. This defect in T-cellfunction greatly contributes to the inability of the host to eliminatethe persisting pathogen. It is disclosed herein that the exhaustion ofvirus-specific T cells is present during persistent LCMV infection ofmice Zajac et al., J Exp Med 188, 2205-2213 (1998); Galimore et al., JExp Med 187, 1383-1393 (1998)) and in other viral infections, includinghuman immunodeficiency virus (HIV), hepatitis B virus (HBV) andhepatitis C virus (HCV) infections in humans (Letvin et al., Nat Med 9,861-866 (2003); Pantaleo et al., Nat Med 10, 806-810 (2004); Rehermannet al., Nat Rev Immunol 5, 215-229 (2005)). The co-inhibitory receptorPD-1 was highly expressed by the exhausted virus-specific CD8 T cells(Barber et al., Nature 439, 682-687 (2006); Sharpe et al., Nat Immunol8, 239-245 (2007)). PD-1 is also upregulated on HIV-1-specific (Petrovaset al., J Exp Med 203, 2281-2292 (2006); Day et al., Nature 443, 350-354(2006)) and SIV-specific (Velu et al., J Virol 81, 5819-5828 (2007)).CD8 T cells and in vitro blockade of PD-1 enhanced cytokine productionand proliferative capacity of these cells. An SIV/macaque model was usedto evaluate the effects of in vivo blockade of PD-1 on the safety andrestoration of virus-specific cellular and humoral immunity duringchronic immunodeficiency virus infections.

PD-1 blockade was performed using an antibody specific to human PD-1that blocks the interaction between macaque PD-1 and its ligands (PDLs)in vitro (Velu et al., J Virol 81, 5819-5828 (2007). Blockade wasperformed during the early (10 weeks) as well as late (˜90 weeks) phasesof chronic SIV infection. Nine macaques (five during the early phase andfour during the late phase) received the anti-PD-1 antibody and fivemacaques (three during the early phase and two during the late phase)received an isotype control antibody (Synagis, anti-Rous sarcoma virus(RSV)-specific) (Malley et al., J Infect Dis 178, 1555-1561 (1998)).

PD-1 blockade during chronic SIV infection resulted in a rapid expansionof SIV-specific CD8 T cells in the blood of all macaques (FIG. 30 a, b).The CD8 T-cell responses to two immunodominant epitopes, Gag CM9 and TatSL8/TL8 (Allen et al., Nature 407, 386-390. (2000)), was studied usingmajor histocompatibility complex (MHC) I tetrameric complexes in sevenof the anti-PD-1-antibody-treated and three of thecontrol-antibody-treated macaques that expressed the Mamu A*01histocompatibility molecule. Most (>98%) of the Gag-CM9tetramer-specific CD8 T cells expressed PD-1 before blockade. After PD-1blockade, the Gag-CM9 tetramer-specific CD8 T cells expanded rapidly andpeaked by 7-21 days. At the peak response, these levels were about2.5-11-fold higher than their respective levels on day 0 (P=0.007) andremained elevated until 28-45 days (FIG. 30 b). Similar results wereobserved with blockade during the early as well as late phases ofchronic SIV infection. A 3-4-fold increase in the frequency ofGag-specific interferon (IFN)-γ-positive CD8 T cells was also observedby day 14 after blockade in the two Mamu A*01-negative animals (RTd11and RDb11), demonstrating that PD-1 blockade can enhance the frequencyof virus-specific CD8 T cells that are restricted by non-Mamu A*01alleles. As expected, expansion of SIV-specific CD8 T cells was notobserved in the control-antibody-treated macaques (FIG. 30).

PD-1 blockade was also associated with a significant increase in thefrequency of virus-specific CD8 T cells that were undergoing active celldivision in vivo with improved functional quality (FIG. 30 b).Consistent with the rapid expansion of SIV-specific CD8 T cells, thefrequency of Gag-CM9 tetramer-specific CD8 cells that co-expressed Ki67(marker for proliferating cells) also increased as early as by day 7after blockade (P=0.01). Similarly, an increase in the frequencies ofGag-CM9 tetramer-specific CD8 T cells co-expressing perforin andgranzyme B (cytolytic potential; P=0.001 and P=0.03, respectively), CD28(co-stimulation potential; P=0.001), CD127 (proliferative potential;P=0.0003) (Kaech et al., Nat Immunol 4, 1191-1198 (2003)) and CCR7(lymph-node homing potential; P=0.001) was observed (Salusto et al,Nature 401, 708-712. (1999)). A transient 1.5-2-fold increase in thefrequency of tetramer-negative and Ki67-positive CD8 T cells afterblockade was also observed. This could be due to expansion of CD8 Tcells specific to other epitopes in Gag as well as other proteins ofSIV, and other chronic viral infections in these animals. No significantenhancement was observed for these markers in the threecontrol-antibody-treated macaques.

Notably, no expansion was observed for Tat-TL8-specific CD8 T cellsafter blockade. This could be due to viral escape from recognition byTat-TL8-specific CD8 T cells, as PD-1 blockade is known to result inexpansion of T cells only when they simultaneously receive signalsthrough T-cell receptor. To test this possibility, the viral genomespresent in the plasma just before the initiation of blockade from allthree Mamu A*01-positive macaques that were infected with SIV251 andreceived the blocking antibody during the early phase of infection weresequenced. Indeed, mutations in the viral genome were foundcorresponding to the Tat TL8 epitope region. All these mutations eitherhave been shown or predicted to reduce the binding of Tat SL8/TL8peptide to Mamu A*01 MHC molecule and result in escape from recognitionby the Tat-SL8/TL8-specific CD8 T cells (Allen et al., Journal ofImmunology 160, 6062-6071 (1998); Allen et al., Nature 407, 386-390.(2000)). These results suggest that in vivo blockade of PD-1 may notresult in expansion of T cells that are specific to escape mutants ofviral epitopes.

PD-1 blockade also resulted in expansion of Gag-CM9-specific CD8 T cellsat the colorectal mucosal tissue (gut), a preferential site of SIV/HIVreplication (Pierson et al., Annu Rev Immunol 18, 665-708 (2000)) (FIG.30 c). Expansion was not observed for two of the seven macaques,although expansion was evident for one of them in blood. In contrast toblood, the expansion in gut peaked much later by day 42 and ranged from2- to 3-fold compared with their respective day 0 levels (P=0.003).Similar to blood, the Gag-CM9 tetramer-specific cells that co-expressedKi67 (P=0.01), perforin (P=0.03), granzyme B (P=0.01) and CD28 (P=0.01)also increased in the gut after blockade.

PD-1 blockade also enhanced the functional quality of anti-viral CD8 Tcells and resulted in the generation of polyfunctional cells capable ofco-producing the cytokines IFN-γ, tumour-necrosis factor (TNF)-α andinterleukin (IL)-2 (FIG. 31). On the day of initiation of PD-1 blockadeduring the late chronic phase of infection, the frequency ofGag-specific IFN-γ-positive cells was low and they failed to co-expressTNF-α and IL-2 (FIG. 31 a). However, after the blockade, the frequencyof IFN-γ-positive cells increased in all four PD-1 antibody-treatedmacaques (P=0.03) and they acquired the ability to co-express TNF-α andIL-2. The expansion of IFN-γ-positive cells peaked by 14-21 days and thepeak levels were 2-10-fold higher than the respective day 0 levels. Onday 21, about 16% of the total Gag-specific cells co-expressed all threecytokines, and about 30% co-expressed IFN-γ and TNF-α (FIG. 31 b). Thisis in contrast to <1% of the total Gag-specific cells co-expressing allthree cytokines (P=0.01), and about 14% co-expressing IFN-γ and TNF-α onday 0 (P=0.04). Similar results were also observed after blockade duringthe early chronic phase of infection.

Chronic immunodeficiency virus infections are associated with B-celldysfunction (De Milito, Current HIV Research 2, 11-21 (2004); Moir andFaucci, J Allergy Clin Immunol 122, 12-19; quiz 20-11 (2008)) but verylittle is known about the role of PD-1 in regulating B-cellfunction/exhaustion. The B-cell responses after PD-1 blockade inSIV-infected macaques (FIG. 32) was characterized. Analysis of PD-1expression on different B-cell subsets before PD-1 blockade revealedpreferential expression of PD-1 by memory B cells (CD20⁺CD27⁺CD21⁻)compared to naïve B cells (CD20⁺CD27⁻CD21⁺; FIG. 32 a, P<0.001). In vivoblockade of PD-1 resulted in a 2-8-fold increase in the titre ofSIV-specific binding antibody by day 28 after blockade (P<0.001; FIG. 32b).

The proliferation of memory B cells was studied in SIV-infected macaquesthat were treated simultaneously with anti-PD-1 antibody andanti-retroviral therapy and observed a significant increase in Ki67⁺(proliferating) memory, but not naïve, B cells as early as day 3 (FIG.32 c). These results demonstrate the PD-1-PDL pathway's role inregulating B-cell dysfunction during chronic SIV infection.Neutralization assays revealed a twofold increase in titres against theeasily neutralizable laboratory-adapted SIV251 and no increase in titresagainst hard-to-neutralize wild-type SIV251 or SIV239. In two of thenine animals treated with anti-PD-1 antibody, only a minimal (<2-fold)expansion of SIV-specific antibody was observed after blockade. Notably,the frequency of total memory B cells in these two animals was lower(˜40% of total B cells) compared with the remaining seven animals(60-90% of total B cells) before blockade, indicating that the level ofSIV-specific memory B cells before blockade can determine the level ofexpansion of SIV-specific antibody after blockade.

PD-1 blockade resulted in significant reductions in plasma viraemia(P=0.03) and also prolonged the survival of SIV-infected macaques(P=0.001; FIG. 33). In two of the five macaques treated with anti-PD-1antibody during the early chronic phase, viral load declined by day 10and persisted at or below this level until day 90 (FIG. 33 a). In onemacaque viral load declined transiently and in the remaining twomacaques increased transiently and returned to pre-blockade levels. Incontrast to the early chronic phase, all four macaques treated with theanti-PD-1 antibody during the late chronic phase showed a transientincrease in viraemia by day 7, but rapidly reduced the virus load by day21 to levels that were below their respective day 0 levels (FIG. 33 b).However, the viral RNA levels returned to pre-blockade levels by day 43.As expected, no significant reductions in the plasma viral loads wereobserved in any of the five macaques treated with the control antibody(FIG. 33 c). By 21-28 days after blockade, the viral RNA levels in theanti-PD-1-antibody-treated animals were 2-10-fold lower than theirrespective day 0 levels (P=0.03; FIG. 33 d). By day 150 after theblockade, four of the five macaques in the control group were killedowing to AIDS-related symptoms (for example loss of appetite, diarrhoea,weight loss), whereas all nine animals in the anti-PD-1-antibody-treatedgroup had survived (P=0.001; FIG. 33 e).

The observed initial rise in plasma viraemia levels in all of thelate-phase-treated and some of the early-phase-treated animals could bedue to an increase in the frequency of activated CD4 T cells. Thepercentage of Ki67-positive total CD4 T cells was measured, as well asthe frequency of SIV Gag-specific IFN-γ-producing CD4 T cells(preferential targets for virus replication (Douek et al., Nature 417,95-98 (2002)) after blockade. These analyses revealed a transientincrease in the percentage of Ki67-positive CD4 T cells by day 7-14after blockade (P=0.002) and this increase was higher in animals treatedduring the late phase than early phase of infection (P=0.015).Similarly, an increase in the frequency of Gag-specific CD4 T cells wasalso observed, but only in animals treated during the late phase ofinfection. No significant increases were observed for these activatedCD4 T cells in the control-antibody-treated macaques. These resultssuggest that the activated CD4 T cells could have contributed to theobserved initial rise in plasma viraemia levels after blockade.

Before initiation of PD-1 blockade, the set point viral load in plasmaand total CD4 T cells in blood and gut were similar between theanti-PD-1-antibody-treated and control-antibody-treated groups. However,the frequencies of Gag CM9⁺ cells and Gag CM9⁺ cells co-expressingperforin, granzyme B or CD28 were not similar between the two treatmentgroups before in vivo blockade (FIG. 30 b). This raises the possibilitythat these differences could have contributed to the expansion of GagCM9⁺ cells after PD-1 blockade. To study the influence of the frequencyof Gag CM9⁺ cells before blockade on their expansion after blockade, theanti-PD-1-antibody-treated group were divided into two subgroups basedon the frequency of Gag CM9⁺ cells before initiation of blockade suchthat one group has similar levels and the other group has higher levelsof Gag CM9⁺ cells compared with the control-antibody-treated group.These subgroups were then analysed for expansion of CM9⁺ cells afterblockade. Expansion of CM9⁺ cells was evident in both subgroups ofanimals after blockade of PD-1, irrespective of whether they were at lowor high levels before blockade. Similar results were also observed withsubgroup analyses based on the frequency of CM9⁺ cells co-expressingmolecules associated with better T-cell function such as perforin,granzyme B, CCR7, CD127 or CD28. However, there was a trend towardsbetter expansion of CM9⁺CD28⁺ cells in animals with higher levels ofCM9⁺CD28⁺ cells before blockade, suggesting that CD28 expression servesas a biomarker for predicting the outcome of in vivo PD-1 blockade.

To evaluate the safety of PD-1 blockade, an extensive analysis of serumproteins, ions, lipids, liver and kidney enzymes, and complete bloodcount after blockade. These analyses revealed no significant changes forall parameters tested between the anti-PD-1-antibody-treated andcontrol-antibody-treated macaques. Similarly, the levels of anti-nuclearantibodies (ANA) in serum (measure of autoimmunity) also did not changesignificantly after treatment with anti-PD-1 antibody.

TABLE 6 Biochemical parameters of blood after the anti-PD-1 antibodyreatment Post SIV infection, Days after PD-1 Pre blockade* Markersinfection* (n = 5) Biochemical profile (n = 8) Day 0 Day 14 Day 56 ALT(U/L) 16.8 ± 5.0    27 ± 11.6 24.8 ± 7.7  27 ± 7.9 AST (U/L) 33.1 ± 8.2 35.0 ± 8.3 29.8 ± 3.6 49.0 ± 18.5 Alkaline Phosphatase 466 ± 135  410 ±367 367 ± 78 451 ± 89  (U/L) Bilirubin (g/L) 0.2 ± 0.1 0.16 ± 0.1 0.12 ±0.0 0.2 ± 0.2 Creatinine (mg/dL) 0.9 ± 0.1  0.7 ± 0.1 0.66 ± 0.1 0.6 ±0.1 Total protein (g/dL) 7.3 ± 0.3  7.0 ± 0.3 7.24 ± 0.4 6.9 ± 0.4Albumin g/L 4.5 ± 0.3 4.28 ± 0.2  4.1 ± 0.2 4.1 ± 0.2 Globulin (g/dL)2.7 ± 0.2 2.72 ± 0.3 3.14 ± 0.3 2.8 ± 0.2 Albumin/Globulin (ratio) 1.7 ±0.2 1.62 ± 0.2 1.32 ± 0.1 1.4 ± 0.1 Glucose (mg/dL) 82 ± 16 69 ± 8 66 ±9  64 ± 8.0 Cholesterol (mg/dL) 161 ± 32  149 ± 32 145 ± 20 140 ± 18 Trigklyceriods (mg/dL) 58 ± 19  64 ± 12 60 ± 7 73 ± 34 Blood UreaNitrogen 18 ± 3  17 ± 3 17 ± 3 16 ± 3  (mg/dL) Blood urea nitrogen- 21 ±3  24 ± 5 26 ± 5 26 ± 5  creatinine (ratio) Lipase (U/L) 21 ± 17 20 ± 721 ± 9 23 ± 10 Creatinine 428 ± 272  537 ± 303  486 ± 129  462 ± 312**Phosphokinase (U/L) Gamma glutamil 74 ± 23  66 ± 16  58 ± 18 71 ± 15transpeptidase (U/L) Calcium (mg/dl)  10 ± 0.5   10 ± 0.2   10 ± 0.5  10± 0.3 Chloride (mEq/L) 110 ± 3  107 ± 3  108 ± 1  107 ± 2  Potassium(mEq/L)   4 ± 0.3   4 ± 0.2   4 ± 0.1   4 ± 0.6 Sodium (mEq/L) 150 ± 5 149 ± 3  149 ± 1  147 ± 2  Phosphorus (mg/dL)   5 ± 0.9   5 ± 0.6   5 ±0.8   6 ± 0.4 *Values represent mean ± standard deviation **Day 91values were used because of RBC lysis on day 56

TABLE 7 Complete blood count after the anti-PD-1 antibody treatment PostSIV infection, Days after PD-1 Pre blockade* infection* (n = 5) Celltype (n = 8) Day 0 Day 14 Day 56 Red blood cells 5.7 ± 0.3 5.9 ± 0.3 5.4± 0.4 5.9 ± 0.3 (Millions/mm³) Hematocrit (%) 41 ± 1  42 ± 1  38 ± 2  41± 2  While blood cells (per μL) 8500 ± 2171 9260 ± 3685 7500 ± 2068 7800± 1972 Neurtrophils (counts/μL) 3685 ± 1883 3274 ± 2124 2573 ± 865  2028± 1585 Lymphocytes (counts/μL) 4477 ± 1583 4700 ± 1791 4235 ± 1880 5041± 1705 Monocytes (counts/μL)) 166 ± 116 635 ± 374 336 ± 123 350 ± 206Eosinophils (counts/μL) 161 ± 155 591 ± 580 277 ± 275 342 ± 175Basophils (counts/μL) 10 ± 20 29 ± 65 78 ± 78 37 ± 53 Platelets(counts/μL) 341 ± 64  275 ± 45  364 ± 79  241 ± 74  *Values representmean ± standard deviation

In one macaque, the levels of ANA increased about 3-fold by day 10 afterblockade, but returned to day 0 levels by day 56. These resultsdemonstrate that anti-PD-1 antibody treatment during chronic SIVinfection results in no observable toxicity. This is consistent with arecent study that demonstrated the safety of PD-1 blockade in patientswith advanced haematological malignancies (Berger et al., Clin CancerRes 14, 3044-3051 (2008)).

The pharmacokinetics of the partially humanized anti-PD-1 antibody inserum after in vivo blockade was studied. The titre of anti-PD-1antibody rapidly declined between days 14 and 28 after blockade andcoincided with macaques generating antibody response against the mouseimmunoglobulin variable domains of anti-PD-1 antibody. Hence completelyhumanized anti-PD-1 antibody may allow longer periods of treatment thatmay further enhance the efficacy of in vivo blockade.

The results demonstrate that in vivo blockade of PD-1 during chronic SIVinfection is safe and results in rapid expansion and restoration ofSIV-specific polyfunctional CD8 T cells and enhanced B-cell responses.Expansion was observed with blockade performed during the early as wellas late phases of chronic infection even under conditions of high levelsof persisting viraemia and AIDS. Expansion was also observed at thecolorectal mucosal tissue, a preferential site of SIV/HIV replication(Pierson et al., Annu Rev Immunol 18, 665-708 (2000)). Importantly, PD-1blockade resulted in a significant reduction of plasma viral load andalso prolonged the survival of SIV-infected macaques. These results arehighly significant considering the failure of blockade of a relatedco-inhibitory molecule CTLA-4 to expand virus-specific CD8 T cells andto reduce plasma viral load in SIV-infected macaques (Cecchinato et al.J Immunol 180, 5439-5447 (2008)). The therapeutic benefits of PD-1blockade could be improved further by using combination therapy withanti-retrovirals and/or therapeutic vaccination.

Example 28 Materials and Methods for Example 29

Animals, SIV Inoculation and Infection Stages:

Indian rhesus monkeys (Macaca mulatta) and sooty mangabeys wereutilized. SIV infection was performed by intravenous inoculation, andthe animals were grouped by stage of infection into: -acute (2 weekspost infection, p.i.), early chronic (10-12 weeks p.i) and late chronic(≧1.5 years p.i.).

Viral Load Measurements:

Plasma viral load was determined by quantitative real-time PCR aspreviously described (Amara et al., Science 292:69-74, 2001). All viralRNA specimens were extracted and assayed in duplicate, with mean resultsreported and used in the analyses.

Phenotypic Analysis by Flow Cytometry:

Surface lymphocyte stainings were performed using 100 μl whole bloodsamples using multi-parameter, multi-color analysis. Lymphocytes wereobtained from necropsy tissue. The following antibodies were used: mouseanti-human antibodies against CD3 (clone SP34-2), CD21 (clone B-Ly4),CD27 (clone M-T2712), CD80 (clone L307.4), CD11c (clone S-HCL-3), allfrom BD BIODSCIENCES®; CD20 (clone 2H7, eBIOSCIENCES®), CD40 (cloneMAB89, BECKMAN COULTER®), CD95 (clone DX2, CALTAG®) and PD-1 (cloneEH-12). Cells were analyzed on a LSRII flow cytometer and data analyzedwith FLOWJO® software version 8.8.2.

Concanavalin A ELISA to Measure SIV Env-Specific Antibody Titers andAvidity:

Titers of anti-env IgG Ab were measured using envelope proteins producedin transient transfections of 293T cells with DNA/89.6 VLP (51).Briefly, 96-well ELISA plates (Costar, Corning Life Sciences) werecoated with 25 μg/ml concanavalin A (Con A) in 10 mM Hepes buffer andincubated overnight at 4° C. Plates were washed six times with PBScontaining 0.05% Tween-20 (PBS-T), 100 μl of VLP added to each wellfollowed by 1 hour incubation at room temperature, another wash andblocking for 1 hour at room temperature with 100 μl blocking buffer(PBS-T with 4% whey and 5% dry milk) per well. Plates were washed andtest sera serially diluted in PBS-T/4% whey added to duplicate wells andincubated for 1 hour at room temperature. For ELISA assays, the plateswere washed 6 times with PBS-T, and bound Ab detected using horseradishperoxidase-conjugated anti-monkey IgG (Rockland Immunochemicals) andtetramethyl benzene (TMB) substrate (KPL), and reactions stopped with100 μl of 2N H₂SO₄. Each plate included a standard curve generated usinggoat anti-monkey IgG (Rockland Immunochemicals) and rhesus IgG (Accuratechemicals). Standard curves were fitted and sample concentrationsinterpolated as μg of Ab per ml of serum using SOFTMAX® 2.3 software.

Avidity of Ab to viral envelope proteins was determined by measuringresistance of antibody-envelope complexes to elution by the chaotropicagent NaSCN in a modification of the env Ab ELISA. Test sera were addedto the plates in quadruplicates, in 3-fold dilutions starting from1:100. Following binding of test sera in the ConA env eLISA, one set ofduplicates was treated with PBS and the other set with 1.5M NaSCN for 10minutes before washing and detection with horseradishperoxidase-conjugated anti-monkey IgG and TMB substrate. Reactions werestopped with 100 μl of 2N H₂SO₄. The avidity index was calculated bydividing the dilution of the serum that gave an O.D. of 0.5 with NaSCNtreatment by the dilution of serum that gave and O.D. of 0.5 with PBS,multiplied by 100.

Neutralization Assay:

Neutralization was measured as a function of a reduction in luciferase(luc) reporter gene expression after single rounds of infection in5.25.EGFP.Luc.M7 cells (TCLA SIVmac25) and TZM-bl cells (293Tpseudovirus) as previously reported (51, 52). Values reported representthe serum dilution at which relative luminescence units (RLUs) werereduced 50% compared to virus control wells.

Apoptosis Assays:

PBMC form 7 SIV-infected macaques were plated in 96-well round-bottomedtissue culture plates at 2.5×10⁵ cells/well under four different cultureconditions: complete RPMI-1640 medium only (spontaneous apoptosis),complete RPMI-1640 medium+10 ng/ml soluble His-tagged rhFasL (R&DSystems) (Fas-mediated apoptosis) & complete RPMI-1640 medium+10 ng/mlsoluble His-tagged rhFasL+10 μg/ml anti-PD-1 blocking Ab. Plates wereincubated for 24 h at 37° C. after which the cells were stained forCD20, CD27, CD21 and Annexin-V and immediately analyzed on an LSRII flowcytometer.

Huh-7.5 cells (53) were transfected with a plasmid expressing HLA-A2under the CMV promoter with a Neomycin resistance gene. Clones wereselected and propagated, and then subsequently transfected with a secondplasmid (pCDNA3.1-Zeo) expressing the full-length INCYTE® human cDNAPD-L1 (OPEN BIOSYSTEMS®, Huntsville, Ala.). A second round of selectionand propagation of clones resistant to both Neomycin and Zeocin wasperformed. Verification of expression of HLA-A2 and PD-L1 was performedby flow cytometry. The Huh-7.5.A2.PD-L1 cells were used to assessPD-L1-mediated apoptosis of activated memory B cells, with Huh-7.5 cellsas control. Both cell lines were seeded onto separate 24-well plates andincubated at 37° C. a day before the experiment. B cells were isolatedfrom PBMC using NHP-specific CD20 microbeads (Miltenyi Biotec) andisolated B cells were added to the cell lines and plates incubated for24 h at 37° C. after which the cells were stained for CD20, CD27, CD21and Annexin-V and immediately analyzed on an LSRII flow cytometer.

In Vitro PBMC Stimulation and Memory B Cell ELISpot Assays:

PBMC were stimulated and used in memory B cell ELISpot assays usingmodifications of the method described by Crotty et al (23). Briefly,PBMC were plated in sterile 24-well tissue culture plates (Costar) at0.5×10⁶ cells/well in complete RPMI-1640 medium containing β-2mercaptoethanol under 3 different culture conditions-medium only(control); mitogen cocktail-pokeweed mitogen diluted 1:1000, fixedStaphylococcus aureus Cowan strain, SAC (SIGMA( ) diluted 1:10,000 and 6μg/ml CpG ODN-2006 (Qiagen-Operon); mitogen cocktail+10 μg/ml anti-PD-1blocking Ab (clone 1540-29C9, provided by GF) in triplicates. Cells werecultured at 37° C. with 5% CO₂ for 6 days.

On Day 5 of culture, 96-well filter ELISpot plates were coated withaffinity-purified goat anti-monkey IgM and IgG (RocklandImmunochemicals) at 10 μg/ml, and SIVmac239 gp130 at 1 μg/ml, andincubated overnight at 4° C.

On Day 6, plates were washed once with PBS-T and three times with PBSand blocked with RPMI-1640 for 2 h at 37° C. Cultured PBMC were washedtwice, added to the prepared ELISpot plates and incubated at 37° C. for6 hours. Plates were then washed 3× with PBS and 3× with PBS-T andincubated overnight at 4° C. with 1 μg/ml biotin-conjugated anti-monkeyIgM (for detection of total IgM ASC) or 1 μg/ml anti-monkey IgG (fordetection of total IgG and anti-gp130 ASC) diluted in PBS-T/1% FCS.Plates were then washed 4× with PBS-T and incubated at for 1 hour atroom temperature with 5 μg/ml HRP-conjugated Avidin D (Vectorlaboratories) diluted in PBS-T/1% FCS. Plates were washed 4× with anddeveloped using 3-Amino-9-Ethylcarbazole (AEC). Spots on developedplates were counted using an ELISpot plate reader. Data are representedas number of spots (ASC) per 10⁶ PBMC.

Statistical Analyses:

Statistical analyses were performed using GRAPHPAD PRISM®.

Example 29 Memory B Cells and PD-1 in Progression of a Chronic Infection

Four Distinct B Cell Subsets can be Identified in Rhesus MacaquePeripheral Blood:

The rhesus macaque B cell compartment was characterized. Four distinct Bcell subsets in peripheral blood of healthy RM:CD20^(int)/CD21⁺/CD27⁻(naïve), CD20^(int)/CD21⁻/CD27⁺ (resting memory),CD20^(hi)/CD21⁻/CD27⁺ (activated memory) and CD20^(hi)/CD21⁻/CD27⁻(unconventional or tissue memory), all with significantly different meanfluorescence intensity (MFI) of CD20 (P<0.0001). Naïve and activatedmemory B cells were the majority subsets, making up 37% and 36% of totalB cells respectively, followed by tissue (18%) and resting (9%) memory Bcells. Cells were stained for surface IgM and IgD and it was found thatunlike in humans there were virtually no IgM-only cells. The naïve Bcells were evenly split between IgD-only and IgD⁺IgM⁺. All three memorysubsets were made up of ˜20% IgD-only cells; the remaining restingmemory B cells were IgD⁺IgM⁺ (˜50%) and IgD⁻IgM⁻ (˜30%). The activatedmemory B cells were the most class-switched subset, with ˜60% of themIgD⁻IgM⁻ and ˜20% IgD⁺IgM⁺. The tissue-like memory B cells on the otherhand were mostly IgD+IgM+(˜70%) with only ˜10% IgD⁻IgM⁻). Thus, a novelB cell subset was identified for rhesus macaques (RM), which unlike theactivated memory B cell subset lacked CD27 expression, but was alsoCD21⁻. These B cells could be similar to the unique tissue-like memory Bcell subset of cells, whose defining surface marker is theimmuno-regulatory molecule FCRL4 in humans.

To further characterize the subsets, the expression of the activationand differentiation markers CD40, CD80, CD95 and CD11c was assessed.Virtually all naïve and resting memory B cells and >70% of restingmemory B cells were CD40^(hi), while the majority (>70%) of activatedmemory B cells were CD40^(int). Activated memory B cells expressed themost CD80, CD95 and CD11c, closely followed by resting memory B cells.CD11c was only expressed on activated and unconventional memory B cells,with naïve B cells expressing negligible amounts of CD80, CD95 andCD11c.

SIV Infection Leads to Depletion of Activated Memory B Cells:

The intravenous route of SIV infection, which we used in this study, hasbeen associated with a more rapid course of disease progression innon-human primates, with up to 30% of animals inoculated via this routeprogressing to AIDS within six months of infection Animals thatdeveloped AIDS-like symptoms or full-blown AIDS and died by week 24 ofinfection were classified as rapid progressors and all the other animalswere classified as typical progressors. One of the first observablechanges occurring in the B cell compartment following HIV and SIVinfections is a marked decrease in numbers of total B cells but it isnot clear which specific B cell subsets are deleted. It was found thatas early as two weeks following SIV infection, peripheral blood total Bcells were severely depleted, regardless of rate of disease progression.A rebound in numbers of B cells occurred by the twelfth week ofinfection in both rapid and typical progressors, but the B cell numbersremained significantly different from pre-infection levels (P<0.0001).The memory B cells in general were depleted following SIV infection witha significant decrease in percentage and numbers of activated memory Bcells. By 12 weeks post infection, the rapid progressors had lost 82% oftheir activated memory B cells, while the typical progressors had lostonly 23%. In contrast to the rapid progressors, the activated memory Bcell proportions returned to pre-infection levels by week 12 ofinfection in the typical progressors. This striking contrast in degreeof activated memory depletion between rapid and typical progressorsprompted the investigation of whether the depletion of activated memoryB cells has any significance for disease progression and SIVpathogenesis.

Depletion of Activated Memory B Cells is an Early Predictor of RapidDisease Progression:

Set-point viral load (12 weeks post infection) was shown to be a goodpredictor of clinical outcome of SIV infection. The association betweenrapid disease progression and viral load and interestingly was analyzed,both rapid and typical progressors had similar peak (week 2 postinfection) viral loads (P=0.8); set-point viral load in the rapidprogressors was however a log greater than in the typical progressors(P<0.0001). Given that differences were observed in activated memory Bcell proportions as early as 2 weeks post infection, it was hypothesizedthat depletion of activated memory B cells could be a much earlierpredictor of rapid disease progression. Blood central memory(CD28⁺CD95⁺, T_(CM)) and gut CD4⁺ T cells have also been suggested asmarkers of disease progression in SIV infection so comparisons werepreformed of all these markers to evaluate the predictive value of eachone. Two weeks post SIV infection, the rapid progressors hadsignificantly lower proportions of activated memory B cells compared tothe typical progressors and activated memory B cells were the only cellsubset whose distribution was significantly different (P<0.001) betweenrapid and typical progressors. By 12 weeks post infection, the activatedmemory B cells were even further depleted in the rapid progressors(P<0.0001), and significant differences between rapid and typicalprogressors also emerged with respect to proportions of T_(CM) and gutCD4⁺ T cells (P<0.01)(FIG. 3B, bottom panel). To further confirm theusefulness of 2-week depletion of activated memory B cells as an earlymarker of disease progression, correlation analyses were performed ofthe set point (week 12 post SIV infection) viral load versus week 2 andweek 12 percentages of activated memory B cells, gut CD4⁺ T cells andT_(CM) cells. Whereas both week 2 and week 12 activated memory B cellswere inversely correlated with set-point viral loads, only week 12 gutCD4⁺ percentages correlated with set-point viremia, and T_(CM) showed nocorrelation with set-point viremia at all. The loss of activated memoryB cells is therefore an early predictor of rapid disease progression inrhesus macaques (RM), with better early predictive value than peak viralload, T_(CM) and gut CD4⁺ T cells.

Depletion of Activated Memory B Cells in Rapidly Progressing SIVInfection Impairs SIV-Specific Humoral Immune Response and Resistance toOther Non-SIV Infections:

RM with rapidly progressing SIV infection were shown to have lowantibody responses as a consequence of the acute destruction of the Bcell compartment. Opportunistic infections and non-SIV related Ags are asignificant cause of mortality in SIV-infected animals. The loss ofactivated memory B cells could have important consequences for thehumoral immune response of rapidly progressing animals to SIV andnon-SIV Ags. Thus, the serum titers of SIV env-binding Abs were measuredin both rapid and typical progressors; it was found that of the 9 rapidprogressors assayed, only 2 mounted a modest env Ab response by week 12and only 1 of the animals had sustained Ab titers by week 20. Theremaining 7 rapid progressors had undetectable SIV env Ab titers throughweek 20 of infection. The typical progressors on the other handdeveloped strong env Ab responses by 12 weeks post infection, with evenhigher titers by week 20.

Bacterial opportunistic infections are a significant cause of morbidityin SIV-infected animals and the causative agents of these infections areusually flagellated. Serum Ab titers to flagellin (F1iC isolated fromSalmonella typhimurium) were measured as a means to assess the effect ofloss of activated memory B cells on pre-existing humoral immunity.Despite starting off with comparable anti-F1iC Ab titers, the rapidprogressors had significantly lower (P=0.001) titers by week 20 postinfection compared to the typical progressors in which titers wereunchanged (P=0.9) (FIG. 5C). Clinical infection data was analyzed forboth groups over a 6-month period following initial SIV infection and itwas found that a wide variety of other infections occurred in theanimals following SIV infection. These included bacterial(Campylobacter, Shigella, enteropathogenic E. coli), parasitic(Trichomonas, whip worms, Giardia) and yeast (Candida) infections. Rapidprogressors succumbed to these infections as early as 1 month p.i. andby 3 months p.i. >50% of the rapid progressors were infected compared to<10% of the typical progressors. This rate of infection in rapidprogressors was sustained throughout the 6-month period.

In Vitro PD-1 Blockade Decreases Fas-Mediated Apoptosis, and Ligation ofPD-1 Induces Apoptosis of Activated Memory B Cells:

PD-1 is mainly expressed on memory B cells of rhesus macaques.Expression of PD-1 was assessed on all B cell subsets in more detailbefore and after SIV infection, and it was found that a higherproportion of all 3 memory B cell subsets expressed higher amounts (meanfluorescence intensity, MFI) of PD-1 compared to naïve B cells(P<0.001). The activated memory cells not only expressed the highestamounts of PD-1, but also had the highest proportion of PD-1⁺ cellscompared to the other subsets (P<0.001). Following SIV infection,irrespective of disease progression status, there was a preferentialdepletion of PD-1⁺ memory B cells. This raised the possibility that PD-1may play a role in depletion of activated memory B cells.

Memory B cells in HIV-infected humans are primed to undergo bothspontaneous and death receptor-induced apoptosis notably through theFas-FasL pathway, but there is little information on what role theFas-FasL pathway plays in B cell apoptosis during SIV infection. Inorder to determine susceptibility of activated memory B cells toFas-mediated apoptosis and to identify a possible role for PD-1 inactivated memory B cell depletion, PBMC from 7 SIV-infected animals werecultured with and without sFasL in combination with PD-1 blockade andanalyzed Annexin-V expression on activated memory B cells was assessedafter 24 hours of culture. In all 6 animals a significant increase inapoptosis was seen with the addition of sFasL to the cultures, and in 4animals a decrease in FasL-mediated apoptosis was observed followingPD-1 blockade, indicating that PD-1 could contribute to apoptosis ofactivated memory B cells.

To further demonstrate the role of PD-1 on apoptosis of activated memoryB cells, the human hepatoma cell line, Huh-7.5 transfected with PD-L1(Huh-7.5.A2.PD-L1) was used as a source of ligand for thePD-1-expressing activated memory B cells. Expression of PD-L1 asverified by flow cytometry showed no PD-L1 expression in thenon-transfected Huh-7.5 cells (control) compared to >90% PD-L1expression on the Huh-7.5.A2.PD-L1 cells. There was an increased rate ofapoptosis in the activated memory B cells cultured in the presence ofPD-L1 compared to the control wells, in 5 out of 7 animals tested. Inone animal (4) a similar rate of apoptosis was observed with or withoutPD-L1, and in the other animal (3), the rate of spontaneous apoptosiswas >30% and addition of PD-L1 did not significantly alter theapoptosis. Thus PD-1 signaling during SIV infection plays a role inactivated memory B cell apoptosis.

Blocking PD-1-PD-L1 interaction was shown to increase the capacity ofHIV-specific CD8⁺ T cells to proliferate and survive. Thus, the effectof in vitro PD-1 blockade on spontaneous and Fas-mediated activatedmemory B cell apoptosis. The effect of in vitro blockade was assessed onthe ability of memory B cells from SIV-infected animals to survive,proliferate in response to polyclonal stimulation, and differentiateinto antibody-secreting cells (ASC) in a memory B cell ELISPot assay.Blockade resulted in slightly decreased Fas-mediated apoptosis ofactivated memory B cells, but did not have an effect on spontaneousapoptosis. Cells stimulated in the presence of PD-1 blocking Abproliferated better and produced higher numbers of ASC against total IgMand IgG, but also env-specific spots.

RM Activated Memory B Cells have Lower Expression of BAFF-R, which isDecreased Further by SIV Infection:

B cell activating factor belonging to the TNF family, BAFF (also knownas B-lys) is an important regulator of B cell homeostasis (21), andCD21⁻ B cells in cynomolgus macaques were shown to express lowerexpression of one of its receptors, BAFF-R. CD21^(low) B cells of HIVviremic patients were also shown to express lower levels of BAFF-R. Itwas found that activated and tissue memory B cells expressed the lowestlevels of BAFF-R compared to naïve and resting memory B cells.Expression was further decreased 2 weeks post infection butinterestingly was restored by week 12. Thus low expression of BAFF-R maybe a contributing factor in the depletion of activated memory B cells.

In Vitro PD-1 Blockade Increases Memory B Cell Proliferation andAntibody Production:

It was investigated whether the presence of PD-1 on memory B cells wouldaffect their ability to proliferate and differentiate into antibodysecreting cells (ASC). An in vitro elispot assay was designed to trackIgM, IgG and SIV gp130-producing memory B cells based on assays thathave been described. Following polyclonal stimulation, there was asignificant increase in IgM (P<0.05) and IgG (P <0.01) ASC in both early(12 weeks, n=3) and late chronic (>1 year, n=2) infection. Cellsstimulated in the presence of α-PD-1 blocking Ab generally proliferatedbetter and produced a higher number of spots than cells stimulatedwithout blocking Ab. gp130-specific ASC were however detectable only inthe late chronic monkeys and as with the IgM and IgG ASCs, polyclonalstimulation resulted in a significantly higher number of gp130 specificASCs, and blockade of PD-1 further increased the numbers of ASCs.

In Vivo PD-1 Blockade Results in Increased SIV Env Binding AntibodyTiters with Higher Avidity, and Increased Neutralizing Ab Titers:

In Vivo Blockade of PD-1 in rhesus macaques with chronic SIV infectionresulted in increased titers of SIV env binding Abs. The avidity of envAbs following in vivo PD-1 blockade was measured. It was found that notonly were the titers of the env Abs increased, but the avidity of thebinding Abs were also increased in the treated animals. This was not thecase in the control Ab-treated animal in which avidity was decreasedfollowing treatment.

Neutralizing activity was also assessed in the PD-1 treated animals, andit was found that though neutralization against a primary SIV isolatewas not significantly different, neutralization against a TCLA SIVstrain was significantly different in the treated animals, with 2 of theanimals showing 3-6 fold increase in neutralizing Ab titers.

Distribution of B Cell Subsets in Sooty Mangabeys:

Sooty mangabeys, one of the natural hosts of SIV, do not develop AIDSdespite persistent high viral titers comparable to those of rhesusmacaques. This makes SM an interesting ‘control’ model for studies ofpathogenic SIV infection in RM. A cohort of uninfected (n=8) andSIV-infected (n=10) sooty mangabeys (SM) was studied. Healthy SM had farfewer circulating total B cells than healthy RM and unlike in RM, we didnot see a decrease in percentage of circulating total B cells followingSIV infection in SM. Identical B cell subsets were identified in SM, butthe distribution of subsets in SM was very different from that in RM.Naïve B cells constituted the major peripheral blood B cell subset(>40%), and the majority memory B cell subset was the tissue-like memoryB cells and not activated memory B cells as in RM. Like RM, <10% ofcirculating memory B cells in the SM were resting memory B cells butcompared to RM, the percentage of activated memory B cells wassignificantly lower in SM. Following SIV infection, there was nodepletion of activated memory B cells; in fact there was a slightincrease in percentage of both resting and activated memory B cells,although these changes did not reach statistical significance. PD-1expression on B cell subsets of SM, as in the RM, was highest on theactivated memory B cells and unlike in RM, PD-1 expression was equallyhigh on tissue memory B cells. Another significant difference between RMand SM was that unlike in RM, the proportions of PD-1 expressing cellswent up following SIV infection in SM.

Example 30 Method of Determining the Efficacy of a PD-1 Antagonist

The efficacy of a PD-1 antagonist for treating a subject can bedetermined by measuring B cells, such as by measuring the presence ofneutralizing antibodies, the proliferation of memory B cells, naïve Bcells, and/or by measuring CD28+ T cells. Generally, a statisticallysignificant increase in neutralizing antibodies, the proliferation ofmemory B cells, naïve B cells, and/or by measuring CD28+ T cellsindicates that the PD-1 antagonist is effective for treating thesubject. B cells can be measured, for example, as described in U.S. Pat.No. 7,378,276 and/or U.S. Pat. No. 6,376,459, both of which areincorporated herein by reference. PD-1 antagonists include antibodiesthat specifically bind PD-L1 and PD-L2, see for example, U.S. Pat. No.7,432,059.

Determining the efficacy of a PD-1 antagonist involves obtaining abiological sample from the subject. A biological sample, such as a bloodsample or a sample of peripheral blood mononuclear cells is taken from ahuman subject, such as a subject with a persistent infection. Thepresence of proliferating memory B cells, naïve B cells and/or CD28+ Tcells is measured using a FACS analysis. The presence of neutralizingantibodies can be measured, such as by using an ELISA. The proliferatingmemory B cells, naïve B cells and/or CD28+ cells, and/or the presence ofneutralizing antibodies can be compared to a control, such as the in asample from the subject obtained prior to treatment with the PD-1antagonist. A statistical test is performed. A statistically significantincrease in proliferating memory B cells, and/or neutralizing antibodiesand/or CD28+ T cells in the blood sample from the subject followingadministration to the subject in comparison to the control demonstratesthat the PD-1 antagonist is effective for treating the subject. However,naïve B cells are not affected by the administration of the PD-1antagonist.

A number of types of subject are treated and tested. These subjectsinclude a subject with an HIV infection, a subject with an xenotropicmurine leukemia virus-related virus (XMRV) infection, and a subject withan polyomavirus JC infection. The PD-1 antagonist can be administeredwith anti-retroviral therapy, such as for treating HIV and XMRV.Suitable subject also include those with tumors, such as a solid tumoror a lymphoma or a leukemia. These subject can also be administered achemotherapeutic agent and/or a tumor antigen.

It will be apparent that the precise details of the methods orcompositions described may be varied or modified without departing fromthe spirit of the described invention. We claim all such modificationsand variations that fall within the scope and spirit of the claimsbelow.

1. A method for determining the dose of a PD-1 antagonist that is usefulto treat a subject, comprising measuring CD20⁺CD27⁺CD21⁻ memory B cellproliferation and CD20⁺CD21⁺CD27⁻ naïve B cell proliferation in a firstsample from the subject administered the first dose of the PD-1antagonist; comparing proliferation of the CD20⁺CD27⁺CD21⁻ memory Bcells to the proliferation of CD20⁺CD21⁺CD27⁻ naïve B cells; andidentifying the subject has having a significant increase in theproliferation of the CD20⁺CD27⁺CD21⁻ memory B cells and an absence of asignificant increase in proliferation of CD20⁺CD21⁺CD27⁻ naïve B cellsfrom the first sample, thereby determining that the dose of the PD-1antagonist is effective for treating the subject, or identifying thesubject as having an absence of a significant increase in theproliferation of the CD20⁺CD27⁺CD21⁻ memory B cells and an absence of asignificant increase in proliferation of CD20⁺CD21⁺CD27⁻ naïve B cellsfrom the first sample, thereby determining that the dose of the PD-1antagonist is insufficient for treating the subject.
 2. The method ofclaim 1, further comprising measuring proliferation of CD20⁺CD27⁺CD21⁻memory B cells and proliferation of CD20⁺ CD21⁺CD27⁻ naïve B cells in asecond sample from the subject following the administration of thesecond dose; identifying the subject as having an absence of asignificant increase in the proliferation of CD20⁺CD27⁺CD21⁻ memory Bcells and an absence of a significant increase in proliferation ofCD20⁺CD21⁺CD27⁻ naïve B cells from the second sample.
 3. The method ofclaim 2, wherein there is the absence of a significant alteration in theproliferation of memory B cells in the first sample as compared to thecontrol, and wherein the second dose is higher than the first dose. 4.The method of claim 2, wherein there is an increase in the proliferationof memory B cells from the first sample as compared to a control, andwherein the second dose is lower than the first dose.
 5. A method fortreating a subject with a PD-1 antagonist, comprising administering thePD-1 antagonist to the subject; isolating CD20⁺CD27⁺CD21⁻ memory B cellsfrom a sample from the subject administered the PD-1 antagonist whereinsaid isolating comprises detecting expression of CD20, CD27 and CD21;isolating CD20⁺CD21⁺CD27⁻ naïve B cells from a sample from the subjectadministered the PD-1 antagonist, wherein said isolating comprisesdetecting expression of CD20, CD21 and CD27; measuring proliferation ofthe memory B cells and the naïve B cells; identifying the subject ashaving an absence of in proliferation of the memory B cells as comparedto proliferation of the naïve B cells, thereby determining that the PD-1antagonist was not efficacious for inducing the immune response in thesubject; and administering a second dose of the PD-1 antagonist to thesubject.
 6. The method of claim 5, wherein measuring proliferatingmemory B cells comprises measuring the expression of Ki67, measuring theincorporation of bromodeoxyuridine, or the use of fluorescence activatedcells sorting (FACS).
 7. The method of claim 5, wherein the subject hasa persistent viral infection or a tumor.
 8. The methods of claim 5,wherein the subject has the persistent viral infection and wherein thesubject is also administered a viral antigen.
 9. The method of claim 8,wherein the viral infection is an infection with a hepatitis virus, ahuman immunodeficiency virus (HIV), a human T-lymphotrophic virus(HTLV), a herpes virus, an Epstein-Barr virus, or a human papillomavirus.
 10. The method of claim 5, wherein the subject has the tumor andwherein the subject is also administered a tumor antigen.
 11. The methodof claim 1, wherein the PD-1 antagonist is an antibody that specificallybinds PD-1, an antibody that specifically binds PD-L1, or an antibodythat specifically binds PD-L2.
 12. The method of claim 11, wherein theantibody that specifically binds PD-1, the antibody that specificallybinds PD-L1, or the antibody that specifically binds PD-L2 is (1) amonoclonal antibody or a functional fragment thereof, (2) a humanizedantibody or a functional fragment thereof, or (3) an immunoglobulinfusion protein.
 13. A method of inducing an immune response in a humansubject, comprising: administering to the subject a therapeuticallyeffective amount of a PD-1 antagonist; and isolating CD20⁺CD27⁺CD21⁻memory B cells from a sample from the subject, wherein said isolatingcomprises detecting expression of CD20, CD27 and CD21; isolatingCD20⁺CD21⁺CD27⁻ naïve B cells from a sample from the subjectadministered the PD-1 antagonist, wherein said isolating comprisesdetecting expression of CD20, CD21 and CD27 and comprises the use offluorescence activated cell sorting; and quantifying proliferation ofthe memory B cells and the naïve B cells; and identifying the subject ashaving an increase in the proliferation of the CD20⁺CD27⁺CD21⁻ memory Bcells and an absence of a significant increase in the proliferation ofCD20⁺CD21⁺CD27⁻ naïve B cells, thereby producing an immune response tothe antigen of interest in the mammalian subject, wherein the mammaliansubject has a persistent infection with a virus or a tumor.
 14. Themethod of claim 13, wherein the subject has the persistent viralinfection.
 15. The method of claim 13, wherein the subject isimmunosuppressed.
 16. The method of claim 13, wherein the subject has ahepatitis infection.
 17. The method of claim 16, wherein the hepatitisinfection is a hepatitis B infection.
 18. The method of claim 13,wherein the PD-1 antagonist is an antibody that specifically binds PD-1,an antibody that specifically binds PD-L1, an antibody that specificallybinds PD-L2, a small inhibitory anti-PD-1 RNAi, a small inhibitoryanti-PD-L1 RNA, an small inhibitory anti-PD-L2 RNAi, an anti-PD-1antisense RNA, an anti-PD-L1 antisense RNA, an anti-PD-L2 antisense RNA,a dominant negative PD-1 protein, a dominant negative PD-L1 protein, adominant negative PD-L2 protein, a small molecule inhibitor of PD-1, orcombinations thereof.
 19. A method of selecting a PD-1 antagonist ofuse, comprising: contacting a population of cells comprisingCD20⁺CD27⁺CD21⁻ memory B cells with an agent in vitro; and detecting theproliferation of CD20⁺CD27⁺CD21⁻ memory B cells and/or thedifferentiation of CD20⁺CD27⁺CD21⁻ memory B cells into antibodysecreting cells, wherein an increase of the proliferation ofCD20⁺CD27⁺CD21⁻ memory B cells and/or an increase in the differentiationof CD20⁺CD27⁺CD21⁻ memory B cells into antibody secreting cellsindicates that the agent is a PD-1 antagonist.
 20. The method of claim18, wherein the PD-1 antagonist is an antibody that specifically bindsPD-1, an antibody that specifically binds PD-L1, an antibody thatspecifically binds PD-L2, a small inhibitory anti-PD-1 RNAi, a smallinhibitory anti-PD-L1 RNA, an small inhibitory anti-PD-L2 RNAi, ananti-PD-1 antisense RNA, an anti-PD-L1 antisense RNA, an anti-PD-L2antisense RNA, a dominant negative PD-1 protein, a dominant negativePD-L1 protein, a dominant negative PD-L2 protein, a small moleculeinhibitor of PD-1, or combinations thereof.